Contacts of the helix formed by residues 1 - 12 (chain G) in PDB entry 2H4C
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 1 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2G PHE* 1.3 63.6 + - - +
3G PHE* 2.3 42.2 + - - +
4G GLN* 3.1 24.1 + - - +
5G PHE 3.1 22.0 + - - -
52G TYR* 4.9 1.6 - - - -
68G PRO 3.6 17.8 + - - -
70G MET 4.0 9.2 - - - +
71G ALA 2.8 29.8 + - - +
72G THR* 4.1 7.7 - - - +
73G TYR* 3.6 10.3 - - - -
99G ASP* 3.7 6.4 - - - +
32H GLY 2.7 13.2 - - - +
33H GLY* 2.8 35.7 + - - +
34H GLN* 3.4 20.2 + - - +
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Residues in contact with PHE 2 (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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1G ASN* 1.3 69.6 - - - +
3G PHE* 1.3 62.7 + - - +
5G PHE* 4.0 21.3 - + - -
6G ALA* 3.5 6.4 + - - +
48G HIS* 4.6 4.0 - + - -
52G TYR* 3.2 45.3 - + - -
69G LYS* 3.3 50.3 - - + +
30H GLY 3.8 8.7 - - - -
31H TRP* 3.4 59.3 - + + +
32H GLY 2.8 8.3 + - - +
69H LYS* 5.4 13.9 - - + -
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Residues in contact with PHE 3 (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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1G ASN* 2.3 29.0 + - - +
2G PHE* 1.3 69.8 - - - +
4G GLN* 1.3 59.1 + - + +
6G ALA* 3.5 6.2 - - - +
7G GLU* 3.4 20.8 + - - +
27H CYS* 3.7 13.9 - - - -
31H TRP 3.3 13.9 - - - -
32H GLY* 3.0 33.1 + - - -
33H GLY 3.6 2.2 - - - -
34H GLN* 3.2 44.2 - - + +
120H TYR* 3.7 26.2 - - + -
121H SER 4.0 1.1 - - - -
122H ILE* 3.4 40.6 - - + +
126H CYS* 3.7 20.4 - - + -
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Residues in contact with GLN 4 (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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1G ASN* 3.1 18.0 + - - +
3G PHE* 1.3 75.2 - - + +
5G PHE* 1.3 57.5 + - - +
6G ALA 3.0 2.2 - - - -
7G GLU* 2.6 34.4 + - - +
8G MET* 2.8 15.9 + - - +
72G THR* 4.3 10.6 - - - +
73G TYR* 2.4 92.5 + - + +
75G TYR* 4.2 17.2 - - + -
34H GLN* 5.2 3.4 - - - +
122H ILE* 5.6 3.4 - - + -
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Residues in contact with PHE 5 (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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1G ASN 3.1 11.9 + - - +
2G PHE* 4.1 22.0 - + + +
4G GLN* 1.3 74.3 - - - +
6G ALA* 1.3 57.4 + - - +
8G MET* 3.0 6.9 + - + +
9G ILE* 2.8 58.0 + - + +
45G CYS* 6.2 5.2 - - - -
48G HIS* 3.5 29.6 - + - -
99G ASP* 2.9 46.3 + - + +
102G ALA* 3.6 26.2 - - + -
103G ALA 4.4 0.2 - - - -
106G LEU* 4.6 4.9 - - + -
31H TRP* 3.3 26.0 - + - -
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Residues in contact with ALA 6 (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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2G PHE 3.5 11.6 + - - +
3G PHE* 3.5 11.4 - - - +
4G GLN 3.0 0.6 - - - -
5G PHE* 1.3 79.2 - - - +
7G GLU* 1.3 58.6 + - + +
10G VAL* 2.9 37.7 + - + +
18G ALA* 3.6 10.3 - - + -
19G VAL* 3.9 29.4 - - + -
31H TRP* 4.0 7.5 - - + -
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Residues in contact with GLU 7 (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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3G PHE 3.8 10.3 - - - +
4G GLN* 2.6 21.0 + - - +
6G ALA* 1.3 76.1 - - + +
8G MET* 1.3 56.2 + - - -
10G VAL* 4.4 4.8 - - - +
11G LYS* 3.1 29.2 + - - +
75G TYR* 3.0 32.2 + - - +
122H ILE* 4.0 27.2 - - + +
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Residues in contact with MET 8 (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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4G GLN 2.8 18.8 + - - +
5G PHE* 3.0 8.9 + - + +
7G GLU* 1.3 76.9 - - - +
9G ILE* 1.3 65.1 + - - +
11G LYS* 2.7 38.3 - - - +
12G MET* 3.0 9.7 - - - +
73G TYR* 3.5 26.9 - - + +
75G TYR* 3.6 33.9 - - + -
82G ILE* 3.4 32.8 - - + -
96G CYS* 4.2 11.7 - - - +
99G ASP* 4.1 8.7 - - + +
100G ARG* 4.6 3.8 - - - +
103G ALA* 3.5 15.3 - - + -
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Residues in contact with ILE 9 (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* 2.8 56.6 + - + +
8G MET* 1.3 71.5 - - - +
10G VAL* 1.3 54.1 + - - +
12G MET* 2.6 32.9 + - - +
13G THR* 3.2 17.2 + - + +
16G LYS 4.7 0.2 - - - -
18G ALA* 2.9 33.4 - - + +
22G TYR* 3.5 23.1 - - + -
103G ALA* 3.5 11.4 - - - +
106G LEU* 3.7 21.1 - - + -
31H TRP* 3.9 16.6 - - + -
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Residues in contact with VAL 10 (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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6G ALA* 2.9 25.0 + - + +
7G GLU* 4.4 4.7 - - - +
9G ILE* 1.3 78.6 - - - +
11G LYS* 1.3 57.7 + - - +
14G GLY* 2.8 36.4 - - - +
16G LYS 3.7 8.1 - - - -
17G GLU* 3.9 14.4 - - - +
18G ALA* 3.1 28.5 - - + +
19G VAL* 4.4 9.2 - - + +
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Residues in contact with LYS 11 (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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7G GLU 3.1 14.5 + - - +
8G MET* 2.7 36.1 + - - +
10G VAL* 1.3 78.5 - - - +
12G MET* 1.3 69.5 + - + +
14G GLY* 4.0 2.6 + - - -
75G TYR* 3.5 15.0 - - + -
76G SER 3.5 9.9 + - - -
77G PHE* 3.4 47.8 - - + -
82G ILE* 2.8 60.1 - - - +
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Residues in contact with MET 12 (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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8G MET 3.0 18.6 - - - +
9G ILE 2.6 14.5 + - - +
11G LYS* 1.3 80.1 - - + +
13G THR* 1.3 58.9 + - + +
14G GLY* 2.6 14.8 + - - -
77G PHE* 3.7 32.5 - - + -
80G GLY 5.3 2.7 - - - +
81G ASP* 5.7 0.7 - - - -
82G ILE* 4.3 10.1 - - + +
103G ALA* 3.2 31.6 - - + +
104G ILE* 3.5 32.5 - - - -
107G GLY* 4.7 3.4 - - - -
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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