Contacts of the helix formed by residues 24 - 32 (chain G) in PDB entry 6C3P
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 24 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PHE* 3.5 18.0 - - - -
15G TYR* 3.3 25.5 + - - +
16G ARG* 3.5 17.4 + - - +
17G VAL 3.7 11.1 + - - +
18G ASP* 4.0 5.3 + - - +
20G GLY 3.6 3.8 + - - +
21G VAL 3.0 12.7 + - - +
22G LEU 4.1 3.0 - - - +
23G ASN* 1.3 76.4 - - - +
25G GLY* 1.3 59.6 + - - +
26G CYS* 3.1 22.3 + - - +
27G PHE* 2.9 24.1 + - + +
28G VAL* 3.2 12.3 + - - +
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Residues in contact with GLY 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ASN 3.3 6.5 + - - -
24G ASN* 1.3 70.6 + - - +
26G CYS* 1.3 65.3 + - - +
28G VAL* 3.2 12.9 - - - +
29G ASP* 2.9 27.5 + - - +
105G HIS* 5.8 2.0 - - - -
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Residues in contact with CYS 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE* 3.8 14.6 - - + -
5G PHE* 3.3 16.5 - - + -
6G CYS* 2.0 52.9 - - - -
15G TYR* 5.1 9.0 - - - -
16G ARG* 5.1 0.9 - - - -
24G ASN* 3.1 16.1 + - - +
25G GLY* 1.3 74.1 - - - +
27G PHE* 1.3 58.7 + - - +
29G ASP* 3.4 3.1 + - - -
30G ALA* 2.9 26.0 + - - +
105G HIS* 4.9 8.0 - - - -
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Residues in contact with PHE 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 3.9 23.8 - - + -
95C PHE* 3.4 30.2 - + + -
96C ALA* 3.5 34.1 - - + -
18G ASP* 5.7 2.0 - - - +
21G VAL* 3.6 33.7 - - + +
22G LEU* 4.4 15.5 - - + -
24G ASN* 2.9 22.0 + - + +
26G CYS* 1.3 79.8 - - - +
28G VAL* 1.3 63.1 + - + +
30G ALA* 3.2 3.7 + - - +
31G LEU* 2.8 46.4 + - + +
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Residues in contact with VAL 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G LEU* 3.8 24.5 - - + +
24G ASN 3.2 6.9 + - - +
25G GLY* 3.2 22.2 - - - +
27G PHE* 1.3 80.6 - - + +
29G ASP* 1.3 61.0 + - + +
31G LEU* 3.6 10.6 - - + +
32G ASN* 2.5 41.6 + - - +
149G THR 5.8 0.4 - - - +
152G ILE* 4.4 22.2 - - + -
153G LYS* 4.7 24.0 - - + +
156G LYS* 5.2 7.0 - - + -
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Residues in contact with ASP 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G PHE* 4.0 2.0 - - + -
25G GLY 2.9 18.9 + - - +
26G CYS 3.5 6.1 - - - +
28G VAL* 1.3 79.6 - - - +
30G ALA* 1.3 60.3 + - - +
32G ASN* 3.5 18.8 + - - +
33G VAL* 3.6 9.9 - - - +
105G HIS* 2.2 63.4 + - + +
106G LEU* 4.0 2.3 + - - +
109G PRO* 3.2 14.0 - - - +
153G LYS* 5.4 9.7 - - - +
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Residues in contact with ALA 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C MET* 5.4 0.5 - - - +
91C TRP* 3.9 25.2 - - + -
92C LEU* 4.7 9.6 - - + -
95C PHE* 5.1 5.4 - - + -
5G PHE* 3.5 26.6 - - + -
26G CYS 2.9 13.4 + - - +
27G PHE* 3.7 5.4 - - - +
29G ASP* 1.3 73.4 - - - +
31G LEU* 1.3 66.7 + - - +
33G VAL* 2.9 23.5 + - - +
34G VAL* 3.7 7.7 + - - +
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Residues in contact with LEU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 4.0 29.3 - - + +
22G LEU* 6.3 2.0 - - + -
27G PHE* 2.8 34.5 + - + +
28G VAL* 3.6 11.4 - - + +
30G ALA* 1.3 77.1 - - - +
32G ASN* 1.3 58.6 + - - +
33G VAL 3.0 5.4 + - - -
34G VAL* 3.2 23.9 + - + +
35G PRO* 3.2 9.9 - - - +
149G THR* 3.9 26.2 - - + +
152G ILE* 5.4 12.8 - - + -
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Residues in contact with ASN 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G VAL* 2.5 29.5 + - - +
29G ASP* 3.6 10.7 + - - +
30G ALA 3.1 0.4 - - - -
31G LEU* 1.3 74.6 - - - +
33G VAL* 1.3 60.3 + - - +
35G PRO* 3.9 5.3 - - - +
36G HIS* 3.7 23.4 + - - -
109G PRO* 4.6 9.1 - - + +
149G THR* 3.0 42.7 + - - +
150G LYS* 3.7 13.7 + - + +
153G LYS* 3.2 34.9 - - - +
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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