Contacts of the strand formed by residues 32 - 39 (chain C) in PDB entry 6H7L
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 ASN 32 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 3.2 22.9 - - + +
29C PHE 2.7 24.6 + - - +
30C ALA* 3.6 8.7 + - - +
31C LEU* 1.3 72.6 - - - +
33C ILE* 1.3 66.0 + - - +
34C MET* 4.1 5.7 - - - +
52C HIS* 3.2 7.5 + - - -
53C SER* 2.9 31.2 + - - -
71C ARG* 2.9 36.4 + - - +
76C ASN* 4.8 4.4 + - - -
97C VAL* 4.8 2.2 - - + -
98C LYS 3.2 17.3 - - - +
99C ASP* 4.4 1.3 - - - -
100C PHE* 3.9 7.1 - - - -
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Residues in contact with ILE 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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146A PRO* 3.8 28.0 - - + -
147A PHE* 4.2 13.5 - - + -
150A GLN* 5.6 3.1 - - - +
32C ASN* 1.3 78.7 - - - +
34C MET* 1.3 71.5 + - - +
35C GLY* 4.7 0.7 - - - +
50C ALA* 3.9 20.6 - - + -
51C ILE 3.6 12.6 - - - +
52C HIS* 3.8 17.0 - - + -
96C ASN* 3.7 1.5 - - - +
97C VAL* 3.3 5.4 - - - +
98C LYS* 2.8 57.5 + - + +
100C PHE* 3.9 14.1 - - + -
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Residues in contact with MET 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C CYS* 4.2 7.2 - - - +
24C ALA* 3.9 18.6 - - + -
28C ILE* 5.5 1.6 - - + -
32C ASN* 4.1 3.8 - - - +
33C ILE* 1.3 77.6 - - - +
35C GLY* 1.3 57.6 + - - +
50C ALA* 3.6 0.5 - - - -
51C ILE* 2.8 38.9 + - + +
69C ILE* 3.9 0.7 - - - +
71C ARG* 3.3 38.8 - - - +
76C ASN* 3.8 32.3 - - + +
77C THR 4.3 1.8 - - - -
78C VAL* 3.8 39.0 - - + -
96C ASN 3.4 4.3 - - - +
97C VAL* 4.0 19.1 - - + -
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Residues in contact with GLY 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 ILE* 4.2 1.5 - - - +
34C MET* 1.3 77.2 - - - +
36C TRP* 1.3 68.5 + - - -
37C TYR* 4.6 7.0 - - - -
49C ALA 3.3 11.2 - - - -
50C ALA* 4.0 6.5 - - - -
69C ILE* 4.2 2.5 - - - -
78C VAL* 4.8 1.4 - - - +
95C CYS* 3.4 8.5 - - - -
96C ASN* 2.9 36.1 + - - +
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Residues in contact with TRP 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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6C GLU* 3.9 25.6 - - + -
7C SER 5.1 0.7 - - - -
20C LEU* 3.7 43.7 - - + -
21C SER 3.7 6.3 - - - -
22C CYS* 3.6 37.9 - - + -
35C GLY* 1.3 77.9 - - - -
37C TYR* 1.3 62.1 - - - +
47C LEU* 3.7 4.3 - - - +
48C VAL* 2.9 28.1 + - + -
49C ALA 2.7 17.9 + - - +
69C ILE* 3.9 16.4 - - + -
78C VAL* 4.0 14.3 + - + +
79C TYR 4.1 1.0 - - - -
80C LEU* 3.6 43.1 - - + +
93C TYR* 4.2 13.5 - - + -
94C TYR 3.4 18.6 - - - -
95C CYS 4.0 6.3 - - - -
114C THR* 4.7 2.7 - - + -
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Residues in contact with TYR 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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35C GLY* 4.8 5.4 - - - -
36C TRP* 1.3 77.7 - - - +
38C ARG* 1.3 58.6 + - - +
45C ARG* 3.9 14.6 - - + -
46C GLU* 3.3 10.8 - - - +
47C LEU* 3.4 44.8 - - + +
48C VAL* 3.8 3.4 - - - -
50C ALA* 6.1 0.2 - - + -
93C TYR* 3.3 6.9 - - - +
94C TYR* 2.7 35.5 + - + +
96C ASN* 3.4 32.4 + - + -
98C LYS* 3.7 23.9 + - - -
110C TRP* 3.5 34.1 - + + -
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Residues in contact with ARG 38 (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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37C TYR* 1.3 75.1 - - - +
39C GLN* 1.3 60.9 + - - +
40C ALA* 4.2 1.6 - - - +
45C ARG* 3.3 4.3 - - - -
46C GLU* 2.9 66.6 + - + +
48C VAL* 3.4 20.3 - - + +
62C SER* 3.3 27.5 + - - -
63C VAL* 4.0 14.9 - - - +
67C PHE* 4.3 0.8 - - - -
88C GLU* 4.9 4.8 + - - +
89C ASP* 2.9 38.5 + - - +
91C ALA* 4.0 14.4 - - + -
92C VAL 3.3 10.1 - - - +
93C TYR* 3.0 34.2 + - + -
94C TYR* 4.7 1.3 - - - +
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Residues in contact with GLN 39 (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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38C ARG* 1.3 75.3 - - - +
40C ALA* 1.3 63.5 + - - +
41C PRO* 3.9 0.5 - - - +
43C LYS 3.2 26.6 + - - +
44C GLN* 4.2 3.8 - - - +
45C ARG* 4.0 30.2 + - + +
91C ALA* 3.5 3.3 - - - -
92C VAL* 3.0 31.0 + - + +
94C TYR* 4.1 27.5 + - + +
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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