Contacts of the helix formed by residues 4663 - 4681 (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 LYS4663 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4659D TYR* 3.4 39.6 + - + +
4662D LEU* 1.3 84.1 - - + +
4664D VAL* 1.3 63.4 + - - +
4665D PRO 3.4 1.6 - - - -
4666D LEU* 2.9 17.7 + - + +
4667D VAL* 2.9 33.4 + - + +
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Residues in contact with VAL4664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659D TYR* 3.2 35.7 - - + +
4660D ASN* 3.5 31.4 - - - +
4663D LYS* 1.3 76.6 - - - +
4665D PRO* 1.3 64.1 - - + +
4667D VAL* 3.2 7.0 - - + +
4668D ILE* 3.1 33.2 + - + +
4781D ILE* 3.6 42.0 - - + -
4787D PHE* 4.9 2.9 - - + -
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Residues in contact with PRO4665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4238D PHE* 3.2 36.7 - - + -
4660D ASN 3.3 19.7 - - - +
4661D CYS* 4.4 10.8 - - - +
4662D LEU 4.1 6.1 - - - +
4663D LYS 3.7 7.4 - - - +
4664D VAL* 1.3 89.2 - - + +
4666D LEU* 1.3 55.2 + - - +
4668D ILE* 4.0 6.7 - - + +
4669D PHE* 3.2 18.4 + - - +
4712D ASN* 4.4 8.7 - - - +
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Residues in contact with LEU4666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235D ASP* 3.9 33.9 - - + +
4238D PHE* 4.8 6.5 - - + -
4239D GLU* 5.6 10.8 - - + -
4662D LEU 4.6 5.8 + - - +
4663D LYS* 2.9 24.4 + - + +
4665D PRO* 1.3 78.5 - - - +
4667D VAL* 1.3 64.2 + - + +
4668D ILE 3.2 0.2 - - - -
4669D PHE* 3.2 6.6 + - + -
4670D LYS* 2.7 33.8 + - + +
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Residues in contact with VAL4667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659D TYR* 5.2 5.4 - - + +
4663D LYS* 2.9 17.5 + - + +
4664D VAL* 3.2 22.0 - - + +
4666D LEU* 1.3 80.9 - - + +
4668D ILE* 1.3 62.5 + - - +
4670D LYS* 3.6 8.3 + - + +
4671D ARG* 3.2 23.7 + - - +
4780D VAL* 5.6 5.6 - - + +
4781D ILE* 4.2 17.9 - - + -
4784D ASP* 5.8 6.7 - - + -
4786D SER* 4.7 14.1 - - - +
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Residues in contact with ILE4668 (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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4664D VAL* 3.1 22.8 + - + +
4665D PRO* 4.2 6.1 - - + +
4667D VAL* 1.3 77.9 - - - +
4669D PHE* 1.3 58.3 + - - +
4671D ARG* 3.3 4.4 + - + +
4672D GLU* 2.8 30.5 + - + +
4710D PRO* 5.0 5.8 - - + -
4712D ASN* 3.8 27.1 - - + +
4773D TYR* 5.5 3.8 - - + +
4776D TRP* 4.7 26.4 - - + -
4777D LYS* 4.4 16.6 - - + +
4780D VAL* 4.9 9.6 - - + -
4781D ILE* 3.8 26.5 - - + -
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Residues in contact with PHE4669 (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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4231D SER 5.6 0.7 - - - -
4234D GLU* 3.5 43.1 - - + -
4235D ASP* 4.1 11.4 - - + -
4238D PHE* 4.1 20.9 - + + -
4665D PRO 3.2 18.4 + - - +
4666D LEU* 3.2 5.6 + - + +
4668D ILE* 1.3 80.4 - - - +
4670D LYS* 1.3 59.9 + - - +
4672D GLU* 4.4 4.5 - - + +
4673D LYS* 3.0 36.9 + - + +
4712D ASN* 3.2 34.8 - - + -
4713D TYR* 3.8 29.8 - + - -
4714D TRP* 4.2 18.8 - + - -
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Residues in contact with LYS4670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235D ASP* 6.5 0.4 - - + -
4666D LEU* 2.7 27.9 + - + +
4667D VAL* 3.9 10.1 - - + +
4668D ILE 3.3 0.2 - - - -
4669D PHE* 1.3 76.3 - - - +
4671D ARG* 1.3 57.9 + - - +
4673D LYS* 4.3 3.2 - - - +
4674D GLU* 3.8 17.2 + - - +
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Residues in contact with ARG4671 (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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4667D VAL 3.2 16.0 + - - +
4668D ILE* 3.9 4.5 - - - +
4670D LYS* 1.3 76.8 - - - +
4672D GLU* 1.3 59.9 + - - +
4673D LYS 3.2 1.3 - - - -
4674D GLU* 3.3 6.7 + - + +
4675D LEU* 3.0 27.6 + - + +
4696D LYS* 4.1 29.9 + - - +
4700D ASP* 5.9 4.4 - - - +
4776D TRP* 3.9 28.0 - - + +
4780D VAL* 3.4 38.7 - - - +
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Residues in contact with GLU4672 (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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4668D ILE* 2.8 28.2 + - + +
4669D PHE* 4.3 4.9 - - - +
4671D ARG* 1.3 74.0 - - - +
4673D LYS* 1.3 57.5 + - - +
4675D LEU* 3.8 9.2 - - + +
4676D ALA* 2.9 30.1 + - - +
4709D PHE* 6.3 2.5 - - + -
4710D PRO* 5.4 12.3 - - + +
4712D ASN* 5.6 2.0 - - + -
4713D TYR* 4.4 19.1 - - + +
4776D TRP* 5.1 12.3 - - + -
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Residues in contact with LYS4673 (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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4231D SER* 5.3 8.7 - - - +
4669D PHE* 3.0 30.0 + - + +
4670D LYS* 4.5 4.0 - - - +
4672D GLU* 1.3 78.1 - - - +
4674D GLU* 1.3 57.3 + - - +
4676D ALA* 4.0 1.0 - - - +
4677D ARG* 3.0 29.1 + - - +
4713D TYR* 3.6 29.1 + - + -
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Residues in contact with GLU4674 (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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4670D LYS 3.8 13.0 + - - +
4671D ARG* 3.3 12.0 + - + +
4673D LYS* 1.3 77.4 - - - +
4675D LEU* 1.3 59.1 + - - +
4677D ARG* 3.9 4.8 - - - +
4678D LYS* 3.0 27.9 + - - +
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Residues in contact with LEU4675 (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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4671D ARG* 3.0 18.6 + - + +
4672D GLU* 3.8 8.1 - - + +
4673D LYS 3.3 0.2 - - - -
4674D GLU* 1.3 75.9 - - - +
4676D ALA* 1.3 63.9 + - - +
4678D LYS* 3.2 6.4 + - + +
4679D LEU* 3.2 32.9 + - + +
4684D LEU* 3.9 27.8 - - + -
4700D ASP* 4.6 15.3 - - + -
4703D VAL* 3.7 28.5 - - + -
4704D LEU* 4.7 5.8 - - + -
4709D PHE* 3.7 26.5 - - + -
4776D TRP* 4.9 8.5 - - + -
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Residues in contact with ALA4676 (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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4672D GLU 2.9 17.8 + - - +
4673D LYS 4.0 1.1 - - - +
4675D LEU* 1.3 78.1 - - - +
4677D ARG* 1.3 60.1 + - - +
4679D LEU* 3.4 13.8 + - - +
4680D GLU* 3.7 9.4 + - - +
4709D PHE* 6.0 3.8 - - + -
4713D TYR* 4.0 33.2 - - + +
4718D VAL* 3.9 29.1 - - + +
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Residues in contact with ARG4677 (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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4673D LYS 3.0 19.7 + - - +
4674D GLU* 4.1 5.2 - - - +
4676D ALA* 1.3 75.8 - - - +
4678D LYS* 1.3 62.5 + - - +
4680D GLU* 3.6 7.6 + - - +
4681D PHE* 3.4 19.8 + - - +
4713D TYR* 5.3 2.8 + - - +
5017D TRP* 6.4 2.0 - - + -
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Residues in contact with LYS4678 (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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4674D GLU 3.0 19.3 + - - +
4675D LEU* 3.2 12.5 + - + +
4677D ARG* 1.3 75.6 - - - +
4679D LEU* 1.3 62.4 + - + +
4681D PHE* 2.8 27.2 - - - +
4682D ASP 3.4 7.3 - - - +
4683D GLY* 3.3 15.1 - - - -
4684D LEU* 5.5 3.8 - - + +
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Residues in contact with LEU4679 (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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4675D LEU* 3.2 37.3 + - + +
4676D ALA* 3.7 9.4 - - - +
4677D ARG 3.3 0.4 - - - -
4678D LYS* 1.3 77.6 - - - +
4680D GLU* 1.3 64.3 + - - +
4681D PHE 3.2 6.4 - - - +
4683D GLY* 4.8 6.9 + - - -
4684D LEU* 4.5 13.0 - - + -
4686D ILE* 5.9 0.9 - - - +
4704D LEU* 5.1 7.9 - - + -
4709D PHE* 4.1 21.3 - - + -
4718D VAL* 4.0 31.0 - - + +
4719D LYS* 4.8 5.8 - - + -
4722D VAL* 3.7 36.1 - - + +
4726D HIS* 4.9 2.3 - - - -
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Residues in contact with GLU4680 (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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4676D ALA 3.7 6.6 + - - +
4677D ARG* 3.6 10.6 + - - +
4678D LYS 3.4 0.2 - - - -
4679D LEU* 1.3 79.8 - - - +
4681D PHE* 1.3 58.3 + - - +
4718D VAL* 5.8 0.2 - - - +
4721D LYS* 6.4 2.5 - - + -
4722D VAL* 5.7 3.1 - - - +
4725D LYS* 5.3 6.5 - - - +
4726D HIS* 4.3 11.8 + - - -
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Residues in contact with PHE4681 (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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4677D ARG 3.4 13.5 + - - +
4678D LYS* 2.8 15.5 - - - +
4679D LEU 3.2 10.4 - - - +
4680D GLU* 1.3 78.7 - - - +
4682D ASP* 1.3 65.3 + - - +
4683D GLY 3.0 3.1 + - - -
4686D ILE* 5.9 0.2 - - - +
4726D HIS* 4.1 11.2 + - - -
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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
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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