Contacts of the helix formed by residues 698 - 714 (chain D) in PDB entry 2HVH
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 THR 698 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696D GLU 3.1 12.9 + - - +
697D VAL* 1.3 78.0 - - - +
699D PRO* 1.3 76.4 - - + +
700D ASN* 3.8 9.8 + - - +
701D MET* 3.2 33.3 + - - +
702D ARG* 3.1 18.2 + - - +
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Residues in contact with PRO 699 (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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697D VAL 4.5 1.6 - - - +
698D THR* 1.3 90.3 - - + +
700D ASN* 1.3 55.7 + - - +
702D ARG* 3.3 10.0 + - + +
703D ARG* 3.0 50.9 + - - +
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Residues in contact with ASN 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630D LEU* 5.2 7.1 - - - +
698D THR* 3.1 10.9 - - - +
699D PRO* 1.3 79.6 - - - +
701D MET* 1.3 64.3 + - + +
703D ARG* 3.1 32.6 + - - +
704D GLN* 3.2 39.0 + - - +
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Residues in contact with MET 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686D ALA* 3.8 7.8 - - + +
690D PHE* 3.4 65.4 - - + -
692D VAL* 3.5 30.5 - - + -
696D GLU 4.1 6.1 - - - +
697D VAL* 4.1 11.0 - - + -
698D THR* 3.2 32.2 + - - +
700D ASN* 1.3 78.8 - - + +
702D ARG* 1.3 60.2 + - - +
704D GLN* 3.3 3.4 + - - +
705D ALA* 3.0 29.6 + - - +
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Residues in contact with ARG 702 (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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656D GLN* 4.1 1.0 - - - +
680D ASP* 2.7 42.2 + - - -
682D HIS* 3.6 22.0 - - + +
683D THR* 3.9 10.8 - - - +
686D ALA* 4.4 7.1 - - - +
697D VAL* 4.7 6.3 - - + -
698D THR 3.1 12.6 + - - +
699D PRO* 3.6 12.8 - - + +
700D ASN 3.3 0.2 - - - -
701D MET* 1.3 77.4 - - - +
703D ARG* 1.3 55.9 + - - +
705D ALA* 3.4 1.5 + - - +
706D LYS* 2.9 48.5 + - - +
881D DCT 2.8 43.4 + - - -
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Residues in contact with ARG 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D ILE 4.7 3.6 + - - -
629D ARG* 3.2 63.3 + - - +
630D LEU* 5.1 3.2 - - - +
634D ARG* 5.4 4.9 - - - +
699D PRO* 3.0 33.1 + - - +
700D ASN* 3.1 40.4 + - - +
701D MET 3.3 0.4 - - - -
702D ARG* 1.3 76.8 - - + +
704D GLN* 1.3 61.2 + - + +
706D LYS* 3.5 19.8 + - + +
707D ALA* 3.3 20.3 + - - +
881D DCT 5.7 0.3 + - - -
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Residues in contact with GLN 704 (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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690D PHE* 4.1 26.5 - - + -
700D ASN* 3.2 27.8 + - - +
701D MET* 3.3 7.8 + - - +
703D ARG* 1.3 78.1 - - + +
705D ALA* 1.3 56.4 + - - +
707D ALA* 3.3 9.7 + - - +
708D VAL* 3.1 29.0 + - - +
724D ASN 4.9 5.2 - - - +
725D LEU* 4.0 22.2 - - + +
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Residues in contact with ALA 705 (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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682D HIS* 3.3 25.4 - - - +
685D THR* 3.6 9.4 - - + +
686D ALA* 3.5 19.7 - - - +
689D ILE* 4.0 4.4 - - + +
701D MET 3.0 16.3 + - - +
702D ARG 4.0 0.9 - - - +
704D GLN* 1.3 73.7 - - - +
706D LYS* 1.3 61.6 + - - +
708D VAL* 3.5 10.8 - - - +
709D ASN* 2.8 35.2 + - - +
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Residues in contact with LYS 706 (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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682D HIS* 3.3 28.2 + - + +
702D ARG* 2.9 32.8 + - - +
703D ARG* 3.5 18.7 - - + +
705D ALA* 1.3 75.2 - - - +
707D ALA* 1.3 57.9 + - - +
709D ASN* 3.7 1.0 - - - +
710D TYR* 2.9 46.5 + - + -
881D DCT 2.8 80.4 + - + +
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Residues in contact with ALA 707 (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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703D ARG 3.3 9.2 + - - +
704D GLN* 3.3 12.7 + - - +
705D ALA 3.2 0.2 - - - -
706D LYS* 1.3 77.7 - - - +
708D VAL* 1.3 55.0 + - + +
710D TYR* 4.8 1.1 - - - -
711D GLY* 2.8 30.7 + - - -
716D ILE* 5.8 1.4 - - - +
724D ASN* 6.0 2.9 - - - +
881D DCT 4.1 12.5 + - - +
3F 6OG 3.8 28.8 - - - +
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Residues in contact with VAL 708 (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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685D THR* 4.0 9.2 - - + -
689D ILE* 3.6 20.6 - - + -
704D GLN 3.1 15.7 + - - +
705D ALA* 3.1 8.3 + - - +
707D ALA* 1.3 72.9 - - + +
709D ASN* 1.3 66.6 + - - +
711D GLY* 5.1 0.4 - - - -
712D ILE* 3.0 41.0 + - + +
716D ILE* 6.4 1.1 - - - -
721D LEU* 4.1 15.5 - - + -
724D ASN* 6.5 0.2 - - + -
725D LEU* 3.7 24.0 - - + -
735D PHE* 3.8 28.7 - - + -
739D TYR* 5.8 0.2 - - + -
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Residues in contact with ASN 709 (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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659D LEU* 4.3 7.4 - - + +
681D ILE* 3.3 25.9 + - - +
682D HIS* 3.3 32.1 + - + +
685D THR* 2.7 31.4 + - - +
705D ALA 2.8 13.5 + - - +
706D LYS 3.7 3.6 - - - +
708D VAL* 1.3 75.7 - - - +
710D TYR* 1.3 63.1 + - - +
712D ILE* 4.3 0.9 - - - +
713D VAL* 3.3 28.6 + - - +
739D TYR* 2.8 33.1 + - - +
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Residues in contact with TYR 710 (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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656D GLN 3.8 1.2 - - - -
658D GLU* 3.2 39.4 + - + -
659D LEU* 3.3 32.9 + - + +
682D HIS* 3.5 12.6 - + - -
706D LYS* 2.9 36.8 + - + +
707D ALA 4.3 1.3 - - - +
709D ASN* 1.3 75.2 - - - +
711D GLY* 1.3 64.4 + - - +
713D VAL* 3.4 3.4 - - + +
714D TYR* 3.0 49.9 + + + -
881D DCT 2.6 61.1 + + + +
3F 6OG 3.7 17.5 - - + +
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Residues in contact with GLY 711 (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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707D ALA 2.8 23.0 + - - -
708D VAL* 3.9 0.9 - - - -
710D TYR* 1.3 70.0 - - - +
712D ILE* 1.3 65.1 + - - +
714D TYR 3.1 9.4 + - - -
715D GLY 3.1 0.9 + - - -
716D ILE* 3.0 32.2 + - - -
3F 6OG 3.6 26.9 + - - -
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Residues in contact with ILE 712 (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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708D VAL* 3.0 36.4 + - + +
709D ASN 4.3 2.7 - - - +
711D GLY* 1.3 75.1 - - - +
713D VAL* 1.3 62.5 + - - +
714D TYR 3.1 1.0 + - - -
715D GLY* 3.2 11.8 + - - -
716D ILE* 3.7 20.4 + - + +
721D LEU* 4.2 11.0 - - + -
735D PHE* 3.8 23.3 - - + -
736D ILE* 4.3 15.5 - - + -
739D TYR* 3.9 38.8 - - + -
740D PHE* 4.0 17.5 - - + -
750D MET* 3.8 9.4 - - - +
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Residues in contact with VAL 713 (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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659D LEU* 4.6 5.4 - - + -
662D LEU* 3.9 29.6 - - + -
709D ASN 3.3 16.5 + - - +
710D TYR* 3.4 20.2 - - + +
712D ILE* 1.3 75.3 - - - +
714D TYR* 1.3 86.4 + - + +
715D GLY 3.4 0.2 - - - -
739D TYR* 3.9 26.5 - - + +
740D PHE* 5.3 0.2 - - - -
746D VAL* 4.5 7.9 - - + -
750D MET* 3.3 30.7 - - - +
792D MET* 4.3 4.3 - - - +
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Residues in contact with TYR 714 (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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658D GLU* 3.0 27.2 + - - +
662D LEU* 6.1 0.9 - - + -
710D TYR* 3.0 36.9 + + - +
711D GLY 3.1 6.5 + - - +
712D ILE 3.1 1.2 - - - -
713D VAL* 1.3 94.7 - - + +
715D GLY* 1.3 54.9 + - - +
716D ILE 3.7 0.7 - - - -
789D ARG* 3.9 16.5 - - - +
792D MET* 4.1 12.6 - - - -
793D ASN* 3.3 50.4 + - + -
796D ILE* 3.3 28.6 - - + +
881D DCT 4.0 6.3 - - - -
3F 6OG 3.6 39.6 - - + +
4F C 4.3 6.8 - - - +
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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