Contacts of the strand formed by residues 54 - 68 (chain C) in PDB entry 6GR2
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 PRO 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ARG* 4.5 1.8 - - - -
38C VAL 3.4 13.2 - - - +
39C ASN* 3.9 1.3 - - - +
52C VAL* 3.4 8.3 - - + -
53C LEU* 1.3 87.8 - - - +
55C MET* 1.3 57.7 + - - +
185C MET* 3.0 30.3 - - + -
189C ILE* 3.8 32.8 - - + -
198C ALA* 3.5 1.5 - - - -
199C LEU* 2.7 54.9 + - - +
201C ILE* 3.9 10.5 - - + -
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Residues in contact with MET 55 (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 ARG* 3.4 2.9 - - - -
38C VAL* 3.0 52.7 + - + +
40C LEU* 4.6 7.1 - - + +
54C PRO* 1.3 75.8 - - - +
56C ALA* 1.3 63.8 + - - +
57C LEU* 4.0 13.9 - - + -
189C ILE* 3.8 7.4 - - - -
197C HIS 3.8 17.7 - - - +
198C ALA* 4.1 8.1 - - + -
213C LEU* 4.1 20.4 - - - -
220C VAL* 3.9 17.3 - - + -
222C ILE* 5.1 0.2 - - + -
381C SER* 3.7 24.7 - - - +
382C GLN 4.0 9.2 - - - +
383C ALA* 4.0 15.5 - - + -
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Residues in contact with ALA 56 (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 PRO* 3.9 11.9 - - + -
36C GLY 3.5 5.4 - - - -
55C MET* 1.3 77.7 - - - +
57C LEU* 1.3 60.7 + - - +
189C ILE* 3.7 15.2 - - - +
193C GLY* 4.2 11.8 - - - -
197C HIS 4.8 2.0 + - - -
382C GLN 3.5 1.2 - - - +
383C ALA* 3.5 7.3 - - - -
384C ALA 2.8 49.7 + - - +
385C ASP 3.8 13.5 - - - +
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Residues in contact with LEU 57 (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 PRO* 3.2 18.0 - - - +
36C GLY* 2.8 16.7 + - - +
37C ARG 3.6 34.3 - - - +
38C VAL* 3.7 14.8 - - + -
55C MET* 4.0 6.3 - - + -
56C ALA* 1.3 74.1 - - - +
58C GLU* 1.3 62.5 + - - +
59C LEU* 3.2 17.9 - - + +
60C MET* 5.6 0.2 - - - +
139C LEU* 3.8 33.2 - - + -
222C ILE* 3.4 26.5 - - + -
381C SER* 3.7 16.8 - - - +
384C ALA* 3.2 15.4 - - - +
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.3 21.8 - - + +
7C PRO 4.3 8.0 - - - +
57C LEU* 1.3 71.2 - - - +
59C LEU* 1.3 65.7 + - - +
60C MET* 3.6 20.2 + - - +
132C SER* 4.2 1.7 + - - -
380C LEU 4.0 3.3 - - - +
381C SER* 3.1 17.0 + - - +
382C GLN* 3.1 49.6 + - - +
383C ALA 5.8 0.2 - - - -
384C ALA* 4.2 11.2 - - + -
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Residues in contact with LEU 59 (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 ARG 5.1 0.9 - - - +
6C GLN* 3.8 38.1 - - + +
35C PRO* 3.3 5.0 - - - +
36C GLY 2.9 23.0 + - - -
57C LEU* 3.2 15.4 - - + +
58C GLU* 1.3 79.1 - - - +
60C MET* 1.3 58.7 + - - +
132C SER* 3.4 28.5 - - - +
133C VAL* 3.4 17.0 - - + -
134C PRO* 3.8 5.4 - - + -
139C LEU* 3.7 26.2 - - + -
379C TYR* 3.5 34.1 - - + -
381C SER* 5.9 0.7 - - - +
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Residues in contact with MET 60 (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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7C PRO 4.4 4.0 - - - +
8C GLN* 5.1 0.2 - - - -
9C VAL* 4.0 40.2 - - + +
12C LEU* 3.8 23.0 - - + +
33C SER* 3.7 24.9 - - - -
34C ALA 3.6 15.7 - - - +
35C PRO* 4.3 4.9 - - + -
58C GLU 3.8 13.5 - - - +
59C LEU* 1.3 74.8 - - - +
61C THR* 1.3 71.9 + - - +
62C VAL* 4.2 3.1 - - - -
130C VAL 4.1 0.2 - - - +
131C SER* 3.0 3.8 + - - -
132C SER* 2.7 37.8 + - - +
133C VAL* 3.3 7.1 - - - +
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Residues in contact with THR 61 (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 SER* 3.0 5.9 - - - -
34C ALA 2.7 38.3 + - - -
60C MET* 1.3 71.2 - - - +
62C VAL* 1.3 65.8 + - - +
63C LEU* 4.3 0.8 + - + +
129C VAL* 3.6 24.0 - - + -
130C VAL 3.3 10.3 - - - +
131C SER* 3.2 16.7 + - - -
141C SER* 4.6 1.7 + - - -
144C SER* 2.6 34.0 + - - +
145C LEU* 4.0 8.5 + - + +
148C ALA* 3.9 18.2 - - + +
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Residues in contact with VAL 62 (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 VAL* 4.9 2.2 - - + -
12C LEU* 3.7 23.8 - - + -
13C LEU* 4.2 21.1 - - + +
16C ALA* 4.1 19.2 - - + +
32C VAL 3.2 8.7 - - - +
33C SER* 4.0 14.1 - - - -
60C MET* 4.2 12.1 - - + -
61C THR* 1.3 77.7 - - - +
63C LEU* 1.3 63.9 + - - +
64C VAL* 4.2 9.2 - - + -
128C VAL 3.8 1.2 - - - +
129C VAL* 3.7 1.6 - - - -
130C VAL* 2.6 47.8 + - + +
390C LEU* 4.4 7.0 - - + -
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Residues in contact with LEU 63 (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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30C LEU 4.1 0.5 - - - +
31C ALA* 3.4 1.4 - - - -
32C VAL* 2.7 49.1 + - + +
61C THR* 4.2 1.7 + - + -
62C VAL* 1.3 73.7 - - - +
64C VAL* 1.3 64.8 + - - +
75C LEU* 6.5 0.7 - - + -
125C PHE* 5.9 2.9 - - + -
127C ALA* 3.6 24.9 - - + -
128C VAL 3.4 9.0 - - - +
129C VAL* 4.2 18.8 - - + -
145C LEU* 5.2 1.8 - - + -
148C ALA* 4.3 8.1 - - + +
149C THR* 4.1 36.8 - - + +
152C PHE* 3.5 33.1 - - + -
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Residues in contact with VAL 64 (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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13C LEU* 3.7 30.5 - - + -
16C ALA* 3.4 26.2 - - + +
17C ARG* 4.7 2.7 - - + -
20C PHE* 3.8 13.7 - - + -
28C PRO* 3.8 11.2 - - + -
30C LEU 3.1 8.3 - - - +
31C ALA* 3.9 7.0 - - + -
62C VAL* 4.2 2.2 + - + -
63C LEU* 1.3 81.3 - - - +
65C GLY* 1.3 60.1 + - - +
127C ALA* 3.0 3.8 - - - +
128C VAL* 2.9 53.7 + - + -
152C PHE* 5.0 0.2 - - - -
392C LEU* 4.7 2.0 - - + -
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Residues in contact with GLY 65 (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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20C PHE* 3.6 9.0 - - - -
28C PRO* 3.9 1.0 - - - +
29C GLU 3.0 4.7 + - - -
30C LEU* 2.8 35.9 + - - +
64C VAL* 1.3 77.0 - - - +
66C SER* 1.3 61.2 + - - -
126C SER 2.8 15.5 - - - -
152C PHE* 3.8 16.5 - - - -
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Residues in contact with SER 66 (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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20C PHE* 3.7 12.2 - - - -
27C GLU 3.8 2.3 + - - -
28C PRO* 3.5 7.4 - - - +
29C GLU* 2.9 39.9 + - - +
30C LEU* 4.9 0.2 - - - -
65C GLY* 1.3 69.3 + - - -
67C PRO* 1.3 79.0 - - - +
68C ARG* 4.3 0.5 - - - +
125C PHE* 3.2 6.6 - - - +
126C SER* 3.0 30.4 + - - -
152C PHE* 3.9 2.3 - - - -
156C LEU* 4.7 2.5 - - - -
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Residues in contact with PRO 67 (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 GLU* 3.1 25.8 - - - +
30C LEU* 4.3 8.3 - - + -
66C SER* 1.3 92.3 - - - +
68C ARG* 1.3 64.9 + - - +
123C PRO* 4.5 10.8 - - + -
124C GLY 3.4 8.3 - - - +
156C LEU* 4.0 24.8 - - + -
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Residues in contact with ARG 68 (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* 4.4 6.1 - - - -
66C SER 4.3 0.2 - - - +
67C PRO* 1.3 79.4 - - - +
69C LYS* 1.3 60.7 + - - +
70C ASP* 2.7 42.3 + - + +
71C GLY 4.6 0.6 + - - -
72C LEU* 3.5 17.6 + - - +
74C SER* 3.8 17.4 - - - +
123C PRO* 4.2 8.0 - - - +
124C GLY* 2.8 26.2 + - - +
125C PHE* 3.4 20.6 - - - -
126C SER* 2.7 40.8 + - - +
88D LEU* 5.7 2.2 - - - +
89D GLN* 3.1 28.9 + - - +
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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