Contacts of the strand formed by residues 31 - 37 (chain D) in PDB entry 1AO7
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 SER 31 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TYR* 2.5 35.2 + - - -
30D GLN* 1.3 77.5 - - - +
32D PHE* 1.3 65.6 + - - +
33D PHE* 3.5 27.4 - - - -
49D ILE 4.3 2.9 - - - -
50D TYR* 4.7 4.9 - - - -
92D VAL* 3.3 5.2 - - - +
93D THR* 2.8 37.0 + - - +
98D THR 4.9 0.2 + - - -
103E PRO* 4.0 7.6 - - - -
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Residues in contact with PHE 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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24D TYR* 3.4 37.0 - + - -
29D SER* 3.5 23.6 - - - -
30D GLN 3.6 15.5 - - - -
31D SER* 1.3 73.4 - - - +
33D PHE* 1.3 69.6 + - - +
49D ILE* 2.9 55.8 + - + +
50D TYR* 5.1 0.9 - - - -
66D LEU* 3.3 37.7 - - + -
68D LYS* 4.4 9.9 - - + -
73D VAL* 4.4 9.9 - - + -
90D CYS* 6.4 0.2 - - - -
91D ALA 3.5 4.7 - - - +
92D VAL* 3.4 38.4 - - + -
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Residues in contact with PHE 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 SER* 3.5 26.7 - - - -
32D PHE* 1.3 83.2 - - - +
34D TRP* 1.3 72.6 + - - +
35D TYR* 4.0 13.9 - + + -
45D LEU* 3.9 16.4 - - + -
47D MET 3.2 8.7 - - - +
48D SER* 3.3 18.6 - - - -
49D ILE* 5.5 0.2 - - - -
50D TYR* 4.4 1.8 - + - -
73D VAL* 5.5 0.5 - - - +
89D LEU 4.5 0.2 - - - -
90D CYS* 3.6 6.1 - - - -
91D ALA* 2.8 33.8 + - + +
93D THR* 3.7 24.9 - - + -
104D LEU* 3.8 20.9 - - + -
103E PRO* 3.7 25.6 - - + -
105E GLU* 3.4 27.6 - - + -
106E GLN 5.5 0.7 - - - -
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Residues in contact with TRP 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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5D GLN* 3.7 22.0 - - - -
20D LEU* 3.8 23.3 - - + -
21D ASN 4.1 4.3 - - - -
22D CYS* 3.9 28.9 - - + -
33D PHE* 1.3 83.3 - - - +
35D TYR* 1.3 61.3 + - - +
45D LEU* 3.7 4.3 - - - +
46D ILE* 3.0 34.7 + - + -
47D MET* 2.9 31.7 + - + +
49D ILE* 4.7 7.2 - - + -
64D ALA* 4.9 0.9 - - + -
73D VAL* 3.5 18.4 - - + +
74D SER* 3.2 35.4 + - - -
75D LEU* 3.8 18.6 - - + -
88D TYR* 4.2 22.4 - - + -
89D LEU 3.4 14.8 - - - -
90D CYS* 4.1 5.4 - - + -
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Residues in contact with TYR 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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33D PHE* 4.0 15.4 - + + -
34D TRP* 1.3 78.5 - - - +
36D ARG* 1.3 60.4 + - - +
43D PRO* 3.9 22.2 - - + -
44D GLU 3.3 6.3 - - - -
45D LEU* 3.5 41.8 - - + +
46D ILE* 4.2 2.7 - - - -
88D TYR* 3.2 10.2 - - - +
89D LEU* 2.8 48.7 + - + +
91D ALA* 4.0 18.8 - - + -
104D LEU* 5.2 1.5 - - + +
106D PHE* 4.1 12.2 - + - -
106E GLN* 2.6 41.2 + - - +
108E PHE* 3.5 25.2 - + - -
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Residues in contact with ARG 36 (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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35D TYR* 1.3 73.8 - - - +
37D GLN* 1.3 63.2 + - - +
38D TYR* 3.7 39.8 + - + -
42D SER 4.1 1.0 - - - +
43D PRO* 3.8 0.4 - - - +
44D GLU* 2.8 69.7 + - + +
46D ILE* 3.9 19.7 - - + +
62D PHE* 4.0 23.0 - - - -
84D ASP* 4.9 6.0 + - - +
86D ALA* 3.5 18.2 - - + -
87D THR 3.9 2.2 - - - -
88D TYR* 3.6 32.5 + - + -
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Residues in contact with GLN 37 (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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36D ARG* 1.3 74.6 - - - +
38D TYR* 1.3 63.9 + - - +
39D SER* 3.7 1.2 + - - -
40D GLY 6.0 0.2 - - - +
41D LYS 3.1 26.2 - - - +
42D SER 4.2 1.6 - - - -
43D PRO* 3.4 29.5 - - + +
86D ALA* 3.5 3.4 - - - +
87D THR* 2.9 52.8 + - + +
89D LEU* 3.7 25.5 - - + +
37E GLN* 2.9 42.8 + - - -
91E PHE* 3.7 0.3 - - - -
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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