Contacts of the helix formed by residues 3 - 20 (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 SER 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 1.3 63.8 + - - +
5C CYS* 3.5 3.5 + - - +
6C LEU* 3.1 28.7 + - - +
7C GLN* 3.2 22.0 + - - +
32D ALA* 3.5 28.6 - - - +
33D ASP* 3.8 21.3 - - - +
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Residues in contact with LEU 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 1.3 69.0 + - - +
5C CYS* 1.3 67.1 + - - +
7C GLN* 3.3 7.7 + - + +
8C ARG* 2.9 32.2 + - + +
68C TYR 4.9 0.2 - - - +
69C PRO* 3.9 27.6 - - + -
70C SER* 5.4 6.3 - - - +
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Residues in contact with CYS 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 3.6 1.3 - - - +
4C LEU* 1.3 81.0 - - - +
6C LEU* 1.3 59.5 + - - +
8C ARG* 3.4 2.8 + - - +
9C LEU* 3.0 50.1 + - - +
39C GLN* 4.2 5.4 - - - -
64C TYR* 4.9 0.2 - - - -
65C PRO 3.6 22.9 - - - -
66C ASN 3.6 7.2 - - - +
68C TYR* 3.2 31.1 + - - +
69C PRO* 4.5 1.3 - - - -
32D ALA* 3.5 27.4 - - + -
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Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 3.1 17.0 + - - +
5C CYS* 1.3 76.2 - - - +
7C GLN* 1.3 61.1 + - - +
9C LEU* 3.8 10.1 - - + +
10C GLN* 3.0 34.6 + - + +
38C LEU* 4.0 22.7 - - + +
39C GLN* 3.8 37.7 - - + +
31D LYS* 5.7 4.5 - - + -
32D ALA* 4.0 5.4 - - + +
33D ASP* 3.8 35.0 - - + +
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Residues in contact with GLN 7 (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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3C SER 3.2 18.4 + - - +
4C LEU* 3.6 9.1 - - + +
6C LEU* 1.3 79.0 - - - +
8C ARG* 1.3 61.5 + - - +
10C GLN* 3.4 10.5 + - - +
11C GLU* 2.8 56.8 + - - +
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Residues in contact with ARG 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 2.9 23.7 + - + +
5C CYS 3.6 4.5 - - - +
7C GLN* 1.3 75.7 + - - +
9C LEU* 1.3 57.6 - - - +
11C GLU* 3.2 22.6 + - - +
12C GLU* 2.8 52.2 + - - +
68C TYR* 3.6 25.9 + - + +
69C PRO* 3.6 23.4 - - + +
105C PRO* 2.8 31.3 + - - +
106C ALA* 3.5 11.0 + - - +
107C ILE 2.9 22.4 + - - -
108C THR* 5.0 0.4 - - - +
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Residues in contact with LEU 9 (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* 3.0 39.8 + - - +
6C LEU* 3.8 9.0 - - + +
7C GLN 3.3 0.2 - - - -
8C ARG* 1.3 72.0 - - - +
10C GLN* 1.3 59.8 + - - +
12C GLU* 3.2 6.6 + - + +
13C ARG* 2.9 30.6 + - - +
38C LEU* 3.3 39.5 - - + +
39C GLN* 3.8 10.1 - - + -
41C TRP* 3.9 11.9 - - + +
64C TYR* 3.6 48.7 - - + -
68C TYR* 3.8 10.1 - - + +
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Residues in contact with GLN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU 3.0 19.6 + - - +
7C GLN* 3.5 16.2 - - - +
9C LEU* 1.3 75.5 - - - +
11C GLU* 1.3 56.6 + - - +
13C ARG* 2.4 52.6 + - - +
14C LYS* 2.9 50.0 + - - +
38C LEU* 3.4 23.3 - - + +
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Residues in contact with GLU 11 (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 GLN* 2.8 45.3 + - - +
8C ARG* 3.2 27.9 + - - +
10C GLN* 1.3 75.0 - - - +
12C GLU* 1.3 58.3 + - - +
14C LYS* 4.4 5.2 - - - +
15C LYS* 2.8 34.1 + - + +
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 2.8 57.8 + - - +
9C LEU* 3.2 13.4 + - + +
11C GLU* 1.3 73.2 - - - +
13C ARG* 1.3 55.1 + - - +
15C LYS* 3.7 12.0 + - - +
16C TRP* 2.8 36.0 + - - +
41C TRP* 4.0 12.7 - - + -
64C TYR* 5.2 3.6 + - - +
68C TYR* 3.7 15.7 - - - +
108C THR* 3.7 13.9 - - - +
109C LEU* 2.9 38.0 + - + +
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Residues in contact with ARG 13 (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 2.9 15.5 + - - +
10C GLN* 2.4 41.5 + - - +
12C GLU* 1.3 73.5 - - - +
14C LYS* 1.3 80.7 + - - +
15C LYS 3.1 1.1 - - - -
16C TRP* 3.4 2.1 + - - +
17C ARG* 3.0 54.5 + - - +
28C PRO* 4.0 11.2 - - + -
36C MET* 2.8 56.1 - - - +
38C LEU* 3.5 14.6 - - - +
41C TRP* 3.5 19.9 - - + -
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Residues in contact with LYS 14 (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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10C GLN* 2.9 42.5 + - - +
11C GLU* 4.4 4.5 - - - +
13C ARG* 1.3 88.1 - - - +
15C LYS* 1.3 61.5 + - - +
17C ARG* 3.7 14.7 + - - +
18C LYS* 3.8 10.4 + - - +
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU 2.8 22.6 + - - +
12C GLU* 3.7 14.5 + - - +
14C LYS* 1.3 74.2 - - - +
16C TRP* 1.3 68.8 + - - +
17C ARG 3.1 1.6 - - - -
18C LYS* 2.9 15.7 + - - +
19C ASP* 3.2 21.4 + - + +
108C THR* 4.0 35.0 + - - +
110C LYS* 4.6 16.8 - - - +
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Residues in contact with TRP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLU 2.8 22.6 + - - +
13C ARG* 3.4 5.4 + - - +
15C LYS* 1.3 77.3 - - - +
17C ARG* 1.3 62.4 + - + +
18C LYS 3.0 4.3 + - - -
19C ASP 4.8 0.4 - - - +
20C HIS* 2.8 75.0 + + + +
21C PRO* 3.8 15.0 - - + -
24C PHE* 3.8 18.8 - - + -
25C TYR* 3.6 26.6 - - - +
26C ALA* 3.3 40.4 + - + +
41C TRP* 4.7 6.5 - + + -
109C LEU* 4.0 21.1 - - + -
110C LYS* 4.1 16.8 - - + -
113C VAL* 3.8 25.4 - - + -
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Residues in contact with ARG 17 (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 ARG* 3.0 36.5 + - - +
14C LYS* 3.9 10.1 - - - +
15C LYS 3.1 1.4 - - - -
16C TRP* 1.3 84.7 - - + +
18C LYS* 1.3 57.6 + - - +
20C HIS* 4.6 7.5 - - - -
26C ALA 5.1 4.4 + - - -
27C LYS* 3.1 47.3 - - - +
28C PRO* 3.9 12.1 - - - +
36C MET* 4.4 17.6 - - - +
41C TRP* 6.3 0.2 - - - -
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Residues in contact with LYS 18 (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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14C LYS 4.3 6.5 - - - +
15C LYS* 2.9 11.3 + - - +
16C TRP 3.0 0.4 + - - -
17C ARG* 1.3 81.1 - - - +
19C ASP* 1.3 61.6 + - + +
20C HIS* 3.9 3.5 + - - -
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Residues in contact with ASP 19 (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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15C LYS* 3.2 21.0 + - + +
16C TRP* 4.3 0.9 - - - -
18C LYS* 1.3 83.3 - - + +
20C HIS* 1.3 62.6 + - - +
110C LYS* 3.8 28.7 + - - +
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Residues in contact with HIS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 2.8 62.6 + + + +
17C ARG* 4.6 7.7 - - - -
18C LYS 3.9 1.6 - - - -
19C ASP* 1.3 80.0 + - - +
21C PRO* 1.4 99.2 - - + +
22C PHE* 3.5 3.0 + - - -
23C GLY 5.5 0.8 + - - -
24C PHE 3.5 20.7 + - - -
25C TYR* 5.1 0.6 - - - -
110C LYS* 5.1 1.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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