Contacts of the strand formed by residues 30 - 35 (chain D) in PDB entry 3S7K
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 GLN 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D SER* 2.8 34.6 + - - +
28D PRO 3.3 1.6 - - - +
29D TRP* 1.3 80.6 - - - +
31D VAL* 1.3 66.7 + - - +
43D GLY* 5.1 3.2 - - - -
44D ALA 4.1 7.4 + - - +
67D ARG 4.4 0.3 - - - +
68D ILE* 3.8 14.4 - - - +
69D GLY 4.0 9.2 + - - +
70D LYS 5.4 4.1 + - - +
139D THR* 2.6 50.5 + - - -
140D GLY* 4.1 4.9 - - - +
141D TRP* 3.6 31.2 - - + -
155D LEU* 3.9 9.5 - - + +
197D GLY* 4.8 2.6 - - - -
198D PRO* 3.8 17.3 - - - +
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Residues in contact with VAL 31 (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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29D TRP 3.5 11.2 - - - +
30D GLN* 1.3 84.4 + - - +
32D MET* 1.3 67.2 + - - +
43D GLY* 3.6 5.0 - - - -
44D ALA* 3.0 47.6 + - + +
45D SER 3.7 4.3 - - - +
46D LEU* 3.6 24.5 - - + +
52D VAL* 4.1 9.9 - - + -
66D VAL* 3.5 37.5 - - + -
67D ARG 3.6 6.5 - - - +
68D ILE* 4.2 12.8 - - + -
141D TRP* 5.3 0.5 - - - -
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Residues in contact with MET 32 (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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31D VAL* 1.3 75.5 - - - +
33D LEU* 1.3 60.1 + - - +
34D PHE* 3.5 37.5 + - + -
40D LEU* 3.8 23.1 - - + -
42D CYS 3.9 3.6 - - - -
43D GLY* 5.0 0.2 - - - -
66D VAL* 3.1 6.4 - - - +
67D ARG* 2.8 39.8 + - - +
70D LYS* 3.6 34.8 - - + -
73D ARG* 4.0 16.4 - - + +
141D TRP* 3.5 50.7 - - + -
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Residues in contact with LEU 33 (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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31D VAL 4.1 1.0 + - - -
32D MET* 1.3 71.6 - - - +
34D PHE* 1.3 59.3 + - - +
40D LEU* 3.5 3.5 - - - +
41D LEU* 2.9 34.7 + - + +
42D CYS* 3.1 35.6 + - + +
43D GLY 4.8 3.8 - - - +
44D ALA* 5.0 2.0 - - + -
54D THR* 5.0 2.9 - - - +
58D CYS* 4.4 11.0 - - + +
59D LEU* 3.7 25.4 - - + -
64D LEU* 4.0 25.6 - - + -
65D LEU 3.7 6.5 - - - +
66D VAL* 3.8 22.0 - - + -
85D LEU* 4.7 0.7 - - + -
106D MET* 3.9 24.0 - - + -
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Residues in contact with PHE 34 (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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32D MET* 3.5 45.8 - - + -
33D LEU* 1.3 77.0 - - - +
35D ARG* 1.3 64.1 + - - +
38D GLN* 4.1 14.8 - - + +
39D GLU* 3.3 23.8 - - - -
40D LEU* 3.6 19.5 - - + -
41D LEU* 4.1 4.7 - - - -
64D LEU* 3.3 8.7 - - - +
65D LEU* 2.8 52.1 + - + -
67D ARG* 3.4 54.3 - - + -
73D ARG* 4.3 8.7 - - - -
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Residues in contact with ARG 35 (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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34D PHE* 1.3 76.2 - - - +
36D LYS* 1.3 91.4 + - - +
37D PRO* 3.7 17.4 - - - +
38D GLN* 3.5 6.9 - - - +
39D GLU* 2.9 55.0 + - + +
41D LEU* 3.7 23.5 - - + +
60D PHE* 3.6 40.0 + - - +
63D ASP* 3.7 12.3 - - + +
64D LEU* 4.5 0.4 - - - -
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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