Contacts of the helix formed by residues 14 - 20 (chain D) in PDB entry 4ZIA
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 TYR 14 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 4.1 17.0 - - + -
11D ASP* 2.7 36.2 + - + +
13D ARG* 1.3 103.0 + - + +
15D LEU* 1.3 60.7 + - - -
16D GLU 3.3 3.1 - - - -
17D GLN* 3.1 27.7 + - - +
18D LEU* 3.1 18.7 + - - +
115D LEU* 3.9 23.6 - - + +
118D THR* 3.5 32.3 + - + +
119D ALA* 3.4 33.2 - - + -
122D ALA* 3.8 13.6 - - + +
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Residues in contact with LEU 15 (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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72C LEU* 3.5 32.5 - - + +
77C VAL* 3.7 31.9 - - + -
80C GLN* 3.5 7.9 - - - +
8D GLN 5.5 0.4 - - - +
10D LEU* 4.7 15.5 - - + +
11D ASP 3.6 4.2 + - - +
12D THR* 3.5 32.8 + - + +
14D TYR* 1.3 73.8 - - - +
16D GLU* 1.3 66.0 + - - +
18D LEU* 3.0 18.5 + - + +
19D HIS* 2.9 36.5 + - + +
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Residues in contact with GLU 16 (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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68C TYR* 5.5 0.9 + - - -
84C ARG* 2.7 45.6 + - - -
12D THR 4.7 2.0 + - - -
13D ARG 5.0 2.8 + - - +
14D TYR 3.3 0.8 - - - -
15D LEU* 1.3 79.1 - - - +
17D GLN* 1.3 64.4 + - + +
19D HIS* 3.4 7.1 + - - -
20D GLN* 2.9 45.3 + - - +
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Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 3.8 6.3 + - - +
14D TYR* 3.1 36.5 + - - +
16D GLU* 1.3 78.5 - - + +
18D LEU* 1.3 60.8 + - - +
20D GLN* 3.5 14.5 + - - +
21D LEU* 3.3 21.3 + - - +
115D LEU* 3.9 27.3 - - + +
118D THR* 5.9 3.2 - - - +
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Residues in contact with LEU 18 (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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77C VAL* 3.7 27.8 - - + -
4D TRP* 4.7 2.5 - - + -
7D LEU* 3.9 49.1 - - + +
10D LEU* 4.1 6.3 - - + -
14D TYR 3.1 11.1 + - - +
15D LEU* 3.0 16.7 + - + +
17D GLN* 1.3 72.5 - - - +
19D HIS* 1.3 67.1 + - - +
20D GLN 3.0 1.6 - - - -
21D LEU* 2.9 32.8 + - + +
22D TYR* 3.3 32.7 - - + +
28D MET* 4.2 8.7 - - + -
115D LEU* 3.9 10.1 - - + +
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Residues in contact with HIS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 4.0 14.2 + - - -
77C VAL* 3.6 36.3 - - + -
80C GLN* 4.1 12.2 + - + -
81C HIS* 2.9 50.7 + - - +
84C ARG* 3.5 34.7 + - - +
15D LEU* 2.9 34.4 + - + +
16D GLU* 3.4 18.1 + - - +
18D LEU* 1.3 74.9 - - - +
20D GLN* 1.3 60.9 + - - +
21D LEU 3.2 0.6 + - - -
22D TYR* 3.5 12.3 + - - +
28D MET* 3.6 4.0 - - - +
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Residues in contact with GLN 20 (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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84C ARG* 4.0 8.7 - - - +
16D GLU* 2.9 46.4 + - - +
17D GLN* 3.8 10.1 - - - +
18D LEU 3.0 1.2 + - - -
19D HIS* 1.3 75.0 - - - +
21D LEU* 1.3 65.4 - - + +
22D TYR 3.2 9.0 + - - +
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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