Contacts of the helix formed by residues 13 - 24 (chain D) in PDB entry 6C6S
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 GLN 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B C 4.3 15.0 - - - -
28B C 3.4 27.3 - - - -
29B C 4.9 1.1 - - - -
9D CYS* 5.1 0.4 - - - -
10D LYS* 3.3 46.6 + - + +
11D ARG 3.4 7.2 + - - +
12D GLY* 1.3 83.8 - - - +
14D LEU* 1.3 60.6 + - - +
15D GLN* 3.2 3.4 - - - +
16D ARG* 2.8 44.5 + - + +
17D ALA* 2.9 29.9 + - - +
74D GLY* 3.5 11.8 - - - +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D CYS* 4.9 5.6 - - + -
10D LYS 4.6 2.0 + - - -
12D GLY* 3.7 1.6 - - - -
13D GLN* 1.3 77.8 - - - +
15D GLN* 1.3 59.3 + - + +
17D ALA* 3.8 4.7 - - - +
18D GLN* 2.8 49.0 + - - +
30D ALA* 4.0 10.1 - - + -
32D MET* 3.7 19.1 - - + -
49D PRO* 3.8 25.4 - - + -
52D PRO 4.1 7.0 - - - +
53D ASN* 4.0 15.7 - - - +
54D TYR 3.3 26.2 - - - +
55D LEU* 3.7 20.7 - - + +
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Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B C 4.9 19.5 + - - +
13D GLN* 3.2 0.8 - - - +
14D LEU* 1.3 80.8 - - + +
16D ARG* 1.3 57.9 + - - +
18D GLN* 3.3 14.7 + - - +
19D GLU* 2.9 29.4 + - - +
32D MET* 3.5 32.5 - - - +
47D SER 4.9 5.3 + - - -
49D PRO* 5.2 4.8 - - - +
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Residues in contact with ARG 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A G 4.5 7.1 + - - -
27B C 5.6 1.2 + - - -
28B C 4.3 22.0 + - - +
29B C 5.8 1.7 + - - +
10D LYS* 5.0 1.2 - - - +
13D GLN* 2.8 55.0 + - + +
15D GLN* 1.3 75.1 - - - +
17D ALA* 1.3 62.2 + - - +
19D GLU* 3.2 14.2 + - - +
20D HIS* 3.0 48.5 + - + +
73D ARG* 3.7 30.9 - - - +
74D GLY 4.2 7.5 - - - +
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D CYS* 4.3 10.1 - - - -
13D GLN 2.9 11.4 + - - +
14D LEU 4.1 2.2 - - - +
16D ARG* 1.3 76.3 - - - +
18D GLN* 1.3 57.5 + - - +
20D HIS* 3.4 1.8 + - - +
21D LEU* 2.9 36.2 + - + +
55D LEU* 5.1 3.1 - - + -
72D THR* 4.6 0.2 - - - +
73D ARG 3.3 12.2 + - - +
74D GLY* 3.3 33.0 - - - +
75D VAL* 3.9 13.9 - - + -
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Residues in contact with GLN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 2.8 37.2 + - + +
15D GLN* 3.5 25.3 + - - +
17D ALA* 1.3 76.4 - - - +
19D GLU* 1.3 56.6 + - - +
21D LEU* 3.4 1.2 + - - +
22D GLU* 2.9 54.5 + - - +
28D CYS* 4.4 28.7 - - + +
29D LEU 5.8 0.2 - - - +
30D ALA* 5.0 8.3 + - - +
32D MET* 4.0 11.3 - - - +
55D LEU* 4.9 4.4 - - + +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLN 2.9 15.3 + - - +
16D ARG* 3.2 16.6 + - - +
18D GLN* 1.3 75.7 - - - +
20D HIS* 1.3 56.2 - - - +
22D GLU* 3.3 12.8 + - + +
23D ARG* 3.0 59.6 + - + +
481I LEU* 5.2 1.4 - - - +
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Residues in contact with HIS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A T 3.6 21.4 + - - +
16D ARG* 3.0 46.0 + - + +
17D ALA 3.8 4.9 - - - +
19D GLU* 1.3 77.5 - - + +
21D LEU* 1.3 58.2 + - - +
23D ARG* 3.2 30.7 + - - +
24D GLN* 2.9 29.5 + - - +
72D THR* 3.8 16.8 - - + -
73D ARG* 3.3 38.1 - - + +
477I GLU* 3.1 28.9 - - - -
481I LEU* 5.2 0.2 - - + -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.2 14.1 - - + -
17D ALA* 2.9 23.1 + - + +
20D HIS* 1.3 74.2 - - - +
22D GLU* 1.3 59.4 + - - +
24D GLN* 2.9 42.2 - - - +
26D VAL* 3.1 32.1 + - + +
28D CYS* 3.6 20.9 - - - -
55D LEU* 4.6 4.7 - - + -
57D VAL* 4.0 26.0 - - + -
69D ILE* 4.2 10.5 - - + -
72D THR* 3.7 20.9 - - + +
75D VAL* 4.6 8.3 - - + -
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLN* 2.9 43.8 + - + +
19D GLU* 3.8 12.0 - - + +
20D HIS 3.2 0.2 - - - -
21D LEU* 1.3 75.9 - - - +
23D ARG* 1.3 60.3 + - - +
24D GLN 2.9 11.6 - - - +
26D VAL 4.9 2.9 - - - +
28D CYS* 5.2 7.8 - - + +
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Residues in contact with ARG 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A T 4.7 10.7 + - - +
19D GLU* 3.0 52.0 + - + +
20D HIS* 3.2 51.6 + - - +
22D GLU* 1.3 76.1 - - - +
24D GLN* 1.3 60.7 + - - +
481I LEU* 3.5 40.6 - - - +
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A T 3.2 60.0 - - + +
20D HIS 2.9 16.6 + - - +
21D LEU* 2.9 38.2 - - - +
22D GLU* 2.9 14.1 - - - +
23D ARG* 1.3 77.5 - - - +
25D ALA* 1.3 60.6 + - - +
26D VAL* 3.3 8.9 + - + +
64D ILE* 4.6 8.9 - - + +
68D THR* 4.2 11.5 - - - +
69D ILE* 4.3 9.5 - - - +
72D THR* 4.0 6.6 + - - -
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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