Contacts of the strand formed by residues 31 - 37 (chain C) in PDB entry 3T0E
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 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B GLU 5.0 0.7 + - - -
99B GLN* 4.2 38.0 - - + +
102B ALA* 4.7 5.5 - - - +
106B THR* 3.9 26.7 + - + +
26C ILE* 4.3 0.2 - - - +
29C THR* 6.0 1.6 - - - -
30C ASP* 1.3 83.2 - - - +
32C ILE* 1.3 62.4 + - - +
33C HIS* 3.3 25.8 - + + -
48C HIS* 4.6 15.9 - + + -
49C GLY 4.4 5.4 - - - -
50C LEU* 3.7 36.6 - - + -
89C VAL* 3.7 4.7 - - - +
90C TYR 2.9 30.7 + - - +
91C GLY* 4.3 0.4 - - - -
100D ASN* 3.2 26.9 - - - -
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C HIS* 3.0 36.1 - - + +
26C ILE* 4.3 7.9 - - + -
31C TYR* 1.3 73.9 - - - +
33C HIS* 1.3 64.4 + - - +
34C TRP* 4.0 18.6 - - + +
47C ILE 3.8 0.5 - - - +
48C HIS* 3.0 26.3 - - - +
49C GLY 3.4 15.5 + - - +
61C LEU* 4.5 4.0 - - + +
63C ILE* 4.0 18.6 - - + -
67C ARG* 4.3 14.8 - - + +
70C SER* 3.6 24.0 - - - +
87C CYS* 4.2 6.5 - - - -
88C THR 3.8 13.0 - - - +
89C VAL* 5.2 0.7 - - + -
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Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 3.3 36.4 + + + +
32C ILE* 1.3 79.5 + - - +
34C TRP* 1.3 67.0 + - - +
35C TYR* 3.1 43.7 - + + -
45C TYR* 4.5 7.4 - + + -
47C ILE 3.8 3.6 - - - +
48C HIS* 3.9 21.4 + + + +
88C THR* 3.1 40.7 + - - +
90C TYR* 4.1 28.1 - + + +
100D ASN* 5.0 2.8 + - - -
102D PRO* 6.4 0.6 - - - +
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Residues in contact with TRP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLN* 3.6 22.7 - - - -
19C LEU* 3.7 23.3 - - + -
20C PRO 4.0 3.6 - - - -
21C CYS* 3.1 34.5 - - + -
32C ILE* 4.0 12.6 - - + +
33C HIS* 1.3 80.0 - - - +
35C TYR* 1.3 62.4 + - - +
45C TYR* 4.8 0.7 - - - -
46C VAL* 2.9 41.9 + - + +
47C ILE* 3.1 17.9 + - + +
61C LEU* 3.8 26.9 - - + +
70C SER* 4.2 4.4 + - - -
72C LEU* 3.6 44.2 - - + -
85C TYR* 4.2 13.2 - - + -
86C TYR 3.4 16.8 - - - -
87C CYS* 3.7 11.7 - - + -
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C HIS* 3.1 46.0 - + + -
34C TRP* 1.3 74.6 - - - +
36C ARG* 1.3 56.1 + - - +
43C PRO* 4.8 3.8 - - + -
44C GLU* 3.4 9.9 - - - +
45C TYR* 3.4 42.4 - + + -
46C VAL* 5.0 0.2 - - - -
85C TYR* 3.5 2.1 - - - +
86C TYR* 2.5 44.9 + - + +
88C THR* 4.0 9.4 - - + -
90C TYR* 4.8 1.9 - - - -
97C LEU* 3.7 33.8 - - + +
99C PHE* 4.1 24.7 - + + -
102D PRO* 5.6 1.0 - - - +
103D LEU* 4.5 24.0 + - + +
105D PHE* 4.9 8.7 - + - -
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TRP 4.3 0.4 + - - -
35C TYR* 1.3 72.6 - - - +
37C GLN* 1.3 63.2 + - - +
38C LEU* 5.3 5.8 - - - +
43C PRO* 3.3 3.0 - - - +
44C GLU* 2.7 60.1 + - + +
45C TYR 5.2 0.2 + - - -
46C VAL* 4.0 18.7 - - + +
58C MET* 4.7 22.2 + - - +
74C LEU* 6.0 0.9 - - - +
80C ARG 4.0 6.5 + - - -
81C ASP* 3.6 27.5 + - - +
83C ALA* 4.4 9.8 - - + +
84C VAL 3.0 12.3 - - - +
85C TYR* 2.9 51.9 + - + -
86C TYR* 5.1 1.3 - - - -
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 1.3 77.2 - - - +
38C LEU* 1.3 71.8 + - - +
39C PRO* 4.4 5.4 - - - +
41C GLN 3.0 28.6 + - - +
42C GLY 3.7 6.3 - - - +
43C PRO* 3.9 11.4 - - + -
44C GLU* 5.3 0.2 - - - -
83C ALA* 3.1 19.4 - - - +
84C VAL* 2.8 26.1 + - + +
86C TYR* 3.1 35.5 + - + -
36D GLN* 2.8 32.6 - - - +
42D LEU* 4.4 2.5 - - - +
89D PHE* 4.1 2.1 - - - -
91D ILE* 4.0 7.1 - - - +
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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