Contacts of the helix formed by residues 630 - 635 (chain D) in PDB entry 2HHW
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 LEU 630 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579D GLN* 3.5 44.2 - - + +
628D ILE 4.2 1.9 + - - +
629D ARG* 1.3 86.9 - - + +
631D GLU* 1.3 60.5 + - - +
632D GLU* 4.5 1.8 - - + +
633D GLY* 3.2 4.1 + - - +
634D ARG* 2.9 27.9 + - - +
700D ASN* 5.3 10.3 - - - +
27E T 4.1 10.8 - - - +
28E C 4.4 2.2 + - - -
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Residues in contact with GLU 631 (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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629D ARG 4.3 0.8 + - - -
630D LEU* 1.3 71.1 - - - +
632D GLU* 1.3 63.8 + - + +
634D ARG* 3.3 19.8 + - - +
635D LYS* 3.0 48.5 + - - +
873D TYR* 2.6 34.4 + - - -
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Residues in contact with GLU 632 (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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510D GLN* 3.7 16.6 + - - +
576D HIS* 3.1 32.9 + - - -
579D GLN* 3.5 25.2 + - - +
580D LEU* 3.8 9.9 - - + +
583D LEU* 4.1 11.5 - - + +
630D LEU* 3.2 2.3 + - + +
631D GLU* 1.3 79.4 - - + +
633D GLY* 1.3 61.1 + - - +
635D LYS* 3.7 20.7 + - - +
636D ILE* 4.6 2.9 + - - +
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Residues in contact with GLY 633 (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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579D GLN* 4.3 4.5 - - - +
583D LEU* 3.6 22.6 - - - +
627D PRO* 3.3 24.4 - - - +
630D LEU* 3.2 6.6 + - - -
632D GLU* 1.3 75.5 - - - +
634D ARG* 1.3 65.9 + - - +
635D LYS 3.1 2.7 - - - -
636D ILE* 2.9 25.6 + - - +
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Residues in contact with ARG 634 (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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627D PRO* 3.7 12.4 - - - +
628D ILE* 3.6 43.4 + - + +
630D LEU 2.9 16.9 + - - +
631D GLU* 3.3 26.8 + - - +
633D GLY* 1.3 76.9 - - - +
635D LYS* 1.3 60.8 + - - +
637D ARG* 3.0 20.9 + - - +
703D ARG* 5.7 4.4 - - - +
873D TYR* 3.2 32.6 + - + +
876D LYS* 2.6 43.9 + - - +
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Residues in contact with LYS 635 (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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503D MET* 3.8 16.1 - - - +
631D GLU* 3.0 42.9 + - - +
632D GLU* 3.8 15.0 - - - +
633D GLY 3.0 1.0 + - - -
634D ARG* 1.3 72.9 - - - +
636D ILE* 1.3 65.4 + - - +
637D ARG 3.0 0.2 - - - -
638D GLN* 2.8 42.7 + - - +
873D TYR* 4.0 12.6 + - - -
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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