Contacts of the helix formed by residues 4639 - 4661 (chain D) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO4639 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4635D GLY 3.4 19.1 - - - +
4636D TYR* 3.5 13.9 - - + +
4638D GLU* 1.3 94.8 - - + +
4640D ALA* 1.3 60.5 + - - +
4641D LEU* 3.2 1.8 + - + -
4642D ARG* 3.5 7.9 + - + +
4643D CYS* 3.4 20.2 + - - +
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Residues in contact with ALA4640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4574D ILE* 5.9 7.4 - - + -
4636D TYR 3.5 16.5 + - - +
4637D MET* 3.6 12.1 - - - +
4638D GLU 3.1 1.4 - - - -
4639D PRO* 1.3 79.1 - - - +
4641D LEU* 1.3 59.2 + - - +
4642D ARG 3.3 0.2 - - - -
4643D CYS* 3.9 3.6 - - - -
4644D LEU* 3.1 48.2 + - + +
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Residues in contact with LEU4641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4571D ILE* 5.7 3.2 - - - +
4574D ILE* 5.9 9.8 - - + +
4575D LEU* 6.4 2.0 - - + -
4629D PHE* 6.3 3.1 - - + -
4630D LEU* 5.9 7.0 - - + +
4637D MET 4.1 4.1 + - - +
4638D GLU* 3.3 22.5 + - + +
4639D PRO 3.2 1.0 - - - -
4640D ALA* 1.3 78.9 - - - +
4642D ARG* 1.3 62.7 + - + +
4644D LEU* 5.5 0.4 - - - -
4645D SER* 2.5 33.3 + - - -
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Residues in contact with ARG4642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4639D PRO* 3.5 8.7 + - + +
4640D ALA 3.3 0.2 - - - -
4641D LEU* 1.3 89.6 - - + +
4643D CYS* 1.3 62.6 + - - +
4645D SER* 3.4 4.9 + - - -
4646D LEU* 3.3 29.7 - - + +
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Residues in contact with CYS4643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4639D PRO 3.4 14.7 + - - +
4640D ALA* 4.3 4.0 - - - +
4641D LEU 3.4 0.2 - - - -
4642D ARG* 1.3 78.7 - - - +
4644D LEU* 1.3 78.9 + - + +
4645D SER 3.3 0.7 + - - -
4646D LEU* 3.6 4.4 + - - +
4647D LEU* 3.6 23.5 + - - +
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Residues in contact with LEU4644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4567D LEU* 3.7 33.7 - - + +
4570D ALA* 4.7 22.9 - - + +
4571D ILE* 5.0 18.6 - - + +
4640D ALA* 3.1 36.2 + - + +
4641D LEU 5.2 0.2 - - - +
4643D CYS* 1.3 90.5 - - + +
4645D SER* 1.3 64.1 + - - +
4646D LEU 3.4 0.2 - - - -
4647D LEU* 4.1 7.0 - - + +
4648D HIS* 3.4 23.0 + - - +
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Residues in contact with SER4645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4571D ILE* 4.8 15.2 - - - +
4641D LEU 2.5 28.0 + - - -
4642D ARG* 3.4 12.0 + - - -
4644D LEU* 1.3 77.4 - - - +
4646D LEU* 1.3 69.0 + - - +
4648D HIS* 3.8 3.9 + - - +
4649D THR* 3.3 24.1 + - - +
4800D GLY 5.8 2.0 - - - -
4801D HIS* 3.9 16.9 + - - -
4807D PHE* 5.0 12.5 - - - -
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Residues in contact with LEU4646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4642D ARG* 3.3 23.6 - - + +
4643D CYS* 3.6 5.2 + - - +
4644D LEU 3.4 0.4 - - - -
4645D SER* 1.3 80.0 - - - +
4647D LEU* 1.3 62.9 + - - +
4649D THR* 2.6 22.2 + - - +
4650D LEU* 3.2 26.9 + - + +
4801D HIS* 3.6 27.8 - - + +
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Residues in contact with LEU4647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4563D LEU* 4.8 6.3 - - + -
4567D LEU* 3.7 33.7 - - + -
4643D CYS* 3.6 17.8 + - - +
4644D LEU* 4.2 6.1 - - + +
4645D SER 3.5 0.4 - - - -
4646D LEU* 1.3 77.8 - - - +
4648D HIS* 1.3 62.8 + - - +
4649D THR 3.2 0.9 + - - -
4650D LEU* 3.3 7.2 + - + +
4651D VAL* 3.2 37.2 + - + +
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Residues in contact with HIS4648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4564D ALA* 4.9 12.6 - - - -
4567D LEU* 4.2 22.3 - - + +
4568D ALA* 5.0 7.2 - - - +
4571D ILE* 5.9 8.7 - - + -
4644D LEU 3.4 16.2 + - - +
4645D SER* 4.1 6.5 + - - +
4646D LEU 3.3 0.8 - - - -
4647D LEU* 1.3 78.7 - - - +
4649D THR* 1.3 60.9 + - - +
4650D LEU 3.5 0.2 - - - -
4651D VAL* 3.3 19.1 - - + +
4652D ALA* 3.6 11.1 + - - +
4793D TYR* 2.4 42.7 + + - -
4797D SER* 4.3 10.3 + - - -
4807D PHE* 5.6 4.5 - + + -
4810D HIS* 3.3 35.5 + + - +
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Residues in contact with THR4649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4645D SER 3.3 8.6 + - - +
4646D LEU* 2.6 31.0 + - - +
4648D HIS* 1.3 79.3 - - - +
4650D LEU* 1.3 68.9 + - - +
4652D ALA* 3.5 5.7 + - - +
4653D PHE* 3.2 23.0 + - - +
4797D SER* 3.6 32.9 - - - +
4798D LEU* 5.3 5.8 - - + -
4801D HIS* 3.5 25.7 + - + +
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Residues in contact with LEU4650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4646D LEU* 3.2 38.9 + - + +
4647D LEU* 3.3 7.8 + - + +
4649D THR* 1.3 82.4 - - - +
4651D VAL* 1.3 65.5 + - + +
4653D PHE* 3.5 10.6 + - + +
4654D LEU* 3.2 24.3 + - - +
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Residues in contact with VAL4651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4560D LEU* 3.3 50.5 - - + +
4563D LEU* 4.3 25.4 - - + +
4564D ALA* 5.2 7.9 - - + +
4567D LEU* 5.5 0.9 - - + -
4647D LEU* 3.2 37.0 + - + +
4648D HIS* 3.3 22.9 - - + +
4650D LEU* 1.3 78.2 - - + +
4652D ALA* 1.3 61.1 + - + +
4654D LEU* 4.6 2.0 - - - -
4655D CYS* 3.5 5.4 + - - +
4793D TYR* 6.6 0.2 - - + -
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Residues in contact with ALA4652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4648D HIS 3.6 14.6 - - - +
4649D THR* 3.5 5.7 + - - +
4650D LEU 3.2 0.8 - - - -
4651D VAL* 1.3 80.6 - - + +
4653D PHE* 1.3 62.8 + - - +
4655D CYS* 3.4 12.1 + - - +
4656D ILE* 3.3 19.1 + - - +
4793D TYR* 4.3 22.0 - - + -
4794D MET* 4.9 9.5 - - + +
4797D SER* 4.1 18.4 - - - +
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Residues in contact with PHE4653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4649D THR 3.2 17.2 + - - +
4650D LEU* 4.0 10.8 - - + +
4652D ALA* 1.3 75.9 - - - +
4654D LEU* 1.3 65.3 + - - +
4656D ILE* 3.4 32.4 + - + +
4657D ILE* 3.8 8.4 + - + +
4794D MET* 5.8 0.7 - - + -
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Residues in contact with LEU4654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4549D PHE* 5.4 13.2 - - + -
4553D LEU* 4.5 9.1 - - + +
4560D LEU* 3.8 19.4 - - + +
4650D LEU 3.2 16.9 + - - +
4651D VAL* 4.2 1.8 - - - +
4652D ALA 3.3 0.2 - - - -
4653D PHE* 1.3 77.6 - - - +
4655D CYS* 1.3 59.8 + - - +
4657D ILE* 3.4 7.0 + - - +
4658D GLY* 3.0 23.9 + - - -
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Residues in contact with CYS4655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4557D PHE* 5.1 11.4 - - - -
4560D LEU* 3.5 15.2 - - + +
4561D ARG* 4.3 19.3 - - - +
4651D VAL 3.5 12.0 + - - +
4652D ALA* 3.4 12.3 + - - +
4653D PHE 3.3 1.0 - - - -
4654D LEU* 1.3 76.9 - - - +
4656D ILE* 1.3 60.5 + - + +
4658D GLY* 3.8 2.2 - - - +
4659D TYR* 2.8 36.7 + - - +
4790D LEU* 3.8 31.1 - - + +
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Residues in contact with ILE4656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4652D ALA 3.3 18.8 - - - +
4653D PHE* 3.7 32.5 - - + +
4654D LEU 3.2 0.4 - - - -
4655D CYS* 1.3 79.0 - - + +
4657D ILE* 1.3 60.0 + - - +
4659D TYR* 3.5 5.6 + - - +
4660D ASN* 3.3 19.4 + - - +
4787D PHE* 4.4 26.9 - - + -
4790D LEU* 5.3 11.0 - - + +
4791D GLY* 5.9 4.7 - - - -
4794D MET* 3.9 23.6 - - + -
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Residues in contact with ILE4657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4549D PHE* 5.0 17.0 - - + -
4550D LEU* 5.5 12.7 - - + +
4553D LEU* 5.1 2.9 - - + -
4653D PHE* 3.8 9.4 + - + +
4654D LEU* 3.4 8.2 + - - +
4655D CYS 3.4 0.2 - - - -
4656D ILE* 1.3 77.6 - - - +
4658D GLY* 1.3 65.2 + - - +
4660D ASN* 3.2 20.3 + - - +
4661D CYS* 3.9 11.3 + - - -
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Residues in contact with GLY4658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4550D LEU 5.4 1.1 - - - -
4553D LEU* 4.1 29.1 - - - +
4554D SER* 4.2 9.1 - - - -
4557D PHE* 4.9 7.2 - - - -
4654D LEU 3.0 15.6 + - - -
4655D CYS* 3.9 2.5 - - - -
4657D ILE* 1.3 78.5 - - - +
4659D TYR* 1.3 60.6 + - - +
4660D ASN 3.4 0.3 + - - -
4661D CYS* 3.4 7.8 + - - +
4662D LEU* 3.4 17.7 + - - +
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Residues in contact with TYR4659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4557D PHE* 5.4 0.6 - - - +
4655D CYS* 2.8 25.0 + - - +
4656D ILE* 3.9 6.3 - - - +
4658D GLY* 1.3 74.3 - - - +
4660D ASN* 1.3 64.7 + - - +
4661D CYS 3.3 0.3 + - - -
4662D LEU* 3.3 23.0 + - + -
4663D LYS* 3.4 32.6 + - + +
4664D VAL* 3.2 26.8 - - + +
4667D VAL* 5.2 5.2 - - + +
4786D SER* 3.4 32.7 + - - -
4787D PHE* 4.0 31.2 - + + -
4790D LEU* 4.9 22.9 - - + -
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Residues in contact with ASN4660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4656D ILE 3.3 12.6 + - - +
4657D ILE* 3.2 15.6 + - - +
4658D GLY 3.2 0.8 - - - -
4659D TYR* 1.3 78.3 - - - +
4661D CYS* 1.3 65.1 + - - +
4664D VAL* 3.5 23.3 - - - +
4665D PRO* 3.3 18.4 - - - +
4778D PHE* 6.3 1.2 - - - -
4781D ILE* 6.2 1.2 - - - +
4787D PHE* 5.9 4.9 - - + -
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Residues in contact with CYS4661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4550D LEU* 4.2 37.7 - - + +
4554D SER* 4.4 18.1 - - - +
4657D ILE 4.0 11.7 - - - -
4658D GLY 3.4 6.2 + - - +
4660D ASN* 1.3 88.2 - - - +
4662D LEU* 1.3 57.8 + - - +
4665D PRO* 4.2 13.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il