Contacts of the strand formed by residues 22 - 28 (chain D) in PDB entry 3UYT
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 ASP 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LYS* 2.7 44.6 + - + +
16D GLY 3.3 7.0 - - - +
17D SER* 4.0 6.1 - - - +
21D GLY* 1.3 77.3 - - - -
23D ILE* 1.3 64.9 + - - +
24D TYR* 3.8 23.6 + - + -
37D ILE 3.8 1.4 - - - +
39D LEU* 3.5 25.1 + - - +
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Residues in contact with ILE 23 (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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14D LYS* 3.7 5.7 - - - +
15D ILE* 3.2 35.3 + - + +
16D GLY 3.2 7.9 + - - +
17D SER* 4.2 2.5 - - - -
18D GLY 4.1 10.1 - - - +
21D GLY 4.1 5.4 - - - +
22D ASP* 1.3 82.2 - - - +
24D TYR* 1.3 72.5 + - - +
36D ALA* 4.2 3.4 - - + -
37D ILE 3.6 2.9 - - - +
38D LYS* 3.5 22.4 - - + -
295D 0CK 3.2 84.8 - - + +
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Residues in contact with TYR 24 (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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11D LEU* 4.0 25.1 - - + -
12D GLY 3.6 18.4 - - - -
13D ARG* 3.5 2.0 - - - -
14D LYS* 3.7 29.2 - - + +
15D ILE* 4.4 4.0 - - - -
22D ASP* 3.8 35.9 + - + -
23D ILE* 1.3 76.2 - - - +
25D LEU* 1.3 69.7 + - - +
36D ALA* 3.4 6.1 - - - -
37D ILE* 2.9 35.9 + - - +
39D LEU* 3.6 31.0 - - + -
77D TYR* 5.5 3.6 + + - -
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Residues in contact with LEU 25 (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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11D LEU* 4.2 0.5 - - - +
12D GLY* 2.5 33.6 + - - -
13D ARG* 2.9 20.6 + - + +
15D ILE* 3.3 35.1 - - + +
24D TYR* 1.3 78.0 - - - +
26D GLY* 1.3 51.7 + - - +
34D GLU* 3.7 35.9 - - + +
35D VAL 3.8 1.1 - - - -
36D ALA* 5.0 0.4 - - - +
37D ILE* 5.2 0.2 - - - -
84D LEU* 3.8 25.1 - - + -
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Residues in contact with GLY 26 (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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10D ARG* 3.1 13.7 - - - -
11D LEU 4.5 0.2 - - - -
12D GLY* 3.9 3.1 - - - -
25D LEU* 1.3 77.6 - - - +
27D THR* 1.3 60.0 + - - -
34D GLU* 3.1 15.0 - - - +
35D VAL* 2.6 45.1 + - - -
37D ILE* 4.3 4.0 - - - -
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Residues in contact with THR 27 (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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9D TYR* 3.4 0.3 - - - -
10D ARG* 2.6 59.2 + - - +
26D GLY* 1.3 73.7 - - - -
28D ASP* 1.3 73.5 + - - +
29D ILE* 3.3 10.9 + - + +
32D GLY* 4.9 3.8 - - - -
33D GLU 3.3 15.7 - - - +
34D GLU* 2.8 22.8 + - - +
35D VAL* 3.7 4.6 - - - +
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Residues in contact with ASP 28 (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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8D ARG* 3.1 29.0 + - - +
9D TYR* 3.3 27.8 + - + -
27D THR* 1.3 71.0 - - - +
29D ILE* 1.3 61.3 + - - +
30D ALA 3.1 4.5 + - - -
31D ALA* 3.0 25.9 + - + +
32D GLY* 2.8 23.9 + - - -
33D GLU* 2.6 21.7 + - + +
35D VAL* 4.0 7.8 - - + +
69D ARG* 2.8 28.8 + - - +
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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