Contacts of the strand formed by residues 36 - 46 (chain C) in PDB entry 2GJD
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 MET 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ARG* 2.8 51.6 - - - +
17C ARG* 4.4 16.4 - - - +
28C PRO* 3.8 22.7 - - + +
29C VAL 3.7 3.1 - - - -
30C LYS* 3.5 31.6 - - + +
31C LYS* 3.8 13.3 + - - +
34C GLY 5.3 0.2 - - - +
35C SER* 1.3 76.4 + - - +
37C ASP* 1.3 60.9 + - - +
38C LEU* 3.4 12.6 + - + +
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Residues in contact with ASP 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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28C PRO* 3.5 7.6 - - - +
29C VAL* 2.9 28.4 + - + +
31C LYS* 3.9 21.3 - - + +
35C SER 3.8 0.8 + - - -
36C MET* 1.3 71.1 - - - +
38C LEU* 1.3 61.0 + - - +
39C GLN* 3.0 21.7 + - - +
40C LYS* 3.1 41.4 + - - +
37D ASP* 4.9 9.2 - - - +
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Residues in contact with LEU 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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6C LEU* 4.0 33.0 - - + +
9C LEU* 3.3 25.6 - - + +
10C GLN* 3.4 39.9 - - + +
13C ARG* 3.5 37.7 - - - +
28C PRO* 4.2 9.6 - - + -
36C MET* 3.4 10.5 + - + +
37C ASP* 1.3 73.1 + - - +
39C GLN* 1.3 57.6 + - - +
41C TRP* 2.7 26.9 + - - +
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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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5C CYS* 4.2 1.6 - - - -
6C LEU* 3.8 12.5 - - + +
9C LEU* 3.8 16.4 - - + -
37C ASP* 3.0 11.2 + - - +
38C LEU* 1.3 77.7 - - - +
40C LYS* 1.3 60.2 + - - +
63C GLU* 3.5 3.5 - - - +
64C TYR* 2.9 57.1 + - - +
65C PRO 3.5 7.1 - - - +
66C ASN* 2.9 20.5 + - - +
31D LYS* 3.5 16.8 - - - +
32D ALA* 3.0 36.4 - - - +
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Residues in contact with LYS 40 (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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29C VAL* 2.9 47.0 + - + +
37C ASP* 3.1 27.2 + - - +
38C LEU 3.3 1.0 - - - -
39C GLN* 1.3 82.1 - - - +
41C TRP* 1.3 64.9 + - - +
42C GLU* 5.6 2.2 - - - -
61C THR* 5.0 15.3 - - - -
62C VAL 3.4 4.0 - - - +
63C GLU* 4.2 27.8 + - + +
63D GLU* 5.6 3.4 + - - -
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Residues in contact with TRP 41 (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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9C LEU* 3.9 25.5 - - + +
12C GLU* 4.0 8.1 - - + -
13C ARG* 3.5 32.3 - - + -
16C TRP* 4.7 5.8 - + + -
26C ALA* 3.9 12.6 - - + -
27C LYS 3.2 22.9 - - - +
28C PRO* 3.7 28.6 - - + +
29C VAL* 4.1 1.3 - - - -
38C LEU* 2.7 30.9 + - + -
40C LYS* 1.3 79.9 - - - +
42C GLU* 1.3 65.6 + - - +
61C THR* 3.3 8.0 - - - -
62C VAL* 2.9 42.3 + - + +
64C TYR* 3.4 23.9 - + - -
109C LEU* 3.5 30.3 - - + -
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Residues in contact with GLU 42 (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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25C TYR* 4.2 10.3 - - + -
26C ALA* 3.3 1.6 - - - -
27C LYS* 2.8 36.3 + - + +
29C VAL* 3.5 26.7 - - + +
40C LYS* 5.6 2.8 - - - -
41C TRP* 1.3 74.8 - - - +
43C ALA* 1.3 61.2 + - - +
60C ILE 3.5 4.5 - - - +
61C THR* 4.3 17.8 - - + +
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Residues in contact with ALA 43 (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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25C TYR* 3.1 27.0 + - - +
26C ALA* 3.6 13.2 - - + -
41C TRP* 4.3 0.4 + - + -
42C GLU* 1.3 75.9 - - - +
44C GLY* 1.3 58.4 + - - +
59C PRO* 3.4 6.1 - - - +
60C ILE* 2.9 51.9 + - + +
62C VAL* 4.7 8.7 - - + -
109C LEU* 5.7 0.9 - - + -
113C VAL* 4.9 8.3 - - + -
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Residues in contact with GLY 44 (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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24C PHE* 3.4 14.2 - - - +
25C TYR* 2.9 50.0 + - - +
43C ALA* 1.3 75.3 - - - +
45C ILE* 1.3 63.5 + - - +
57C VAL* 4.0 7.9 - - - -
58C TYR 3.4 7.9 - - - -
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Residues in contact with ILE 45 (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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24C PHE* 3.8 4.9 - - + -
44C GLY* 1.3 78.6 - - - +
46C PRO* 1.3 69.3 - - - +
57C VAL* 4.1 1.1 - - - -
58C TYR* 2.8 48.8 + - + +
60C ILE* 4.0 20.6 - - + -
77C PHE* 4.8 1.6 - - + -
113C VAL* 3.5 42.4 - - + +
116C VAL* 4.2 17.0 - - + -
117C GLN* 3.7 37.2 - - + +
120C LEU* 4.1 9.4 - - + -
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Residues in contact with PRO 46 (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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22C PHE 4.3 2.7 - - - +
23C GLY* 3.4 31.0 - - - +
24C PHE* 3.5 41.5 - - + -
44C GLY 3.7 0.9 - - - +
45C ILE* 1.3 87.2 - - - +
47C GLY* 1.3 64.2 + - - +
56C GLY 3.4 9.9 - - - +
57C VAL* 4.2 9.2 - - + -
117C GLN* 2.9 32.6 + - - +
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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