Contacts of the helix formed by residues 5 - 14 (chain U) in PDB entry 1G3I
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 THR 5 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4U MET* 1.3 77.6 - - - +
6U PRO* 1.3 77.2 - - - +
7U ARG* 3.9 7.0 + - + +
8U GLU* 3.0 44.1 - - + +
9U ILE* 2.9 29.9 + - - +
32U ARG* 3.3 9.5 + - - +
412V SER* 3.5 20.1 + - - -
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Residues in contact with PRO 6 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U THR* 1.3 86.1 - - - +
7U ARG* 1.3 59.8 + - + +
8U GLU 2.6 17.4 + - - -
9U ILE* 2.7 24.3 + - + -
10U VAL* 3.0 18.1 + - - +
28U ALA* 3.8 24.9 - - + -
29U ILE* 4.6 2.9 - - + +
32U ARG* 3.4 33.2 - - + +
408V SER 5.1 4.7 - - - +
409V PHE* 4.2 28.0 - - + +
412V SER* 4.9 3.8 - - - +
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Residues in contact with ARG 7 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U THR* 3.5 11.0 - - + +
6U PRO* 1.3 81.6 - - + +
8U GLU* 1.3 60.5 + - + +
10U VAL* 4.0 11.1 - - - +
11U SER* 3.8 13.2 + - - -
409V PHE* 3.5 39.6 - - - +
410V SER* 3.4 31.5 - - - +
412V SER* 5.7 3.6 - - - -
413V ASP* 3.0 39.9 + - - +
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Residues in contact with GLU 8 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U MET* 5.7 6.7 - - + +
5U THR* 3.0 32.0 + - + +
6U PRO 2.6 5.3 + - - -
7U ARG* 1.3 78.5 - - + +
9U ILE* 1.3 65.5 + - - +
10U VAL 2.9 2.9 + - - -
11U SER* 3.0 17.9 + - - +
12U GLU* 3.0 13.5 + - - +
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Residues in contact with ILE 9 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U MET* 4.8 13.9 - - + -
5U THR* 2.9 37.1 + - - +
6U PRO* 2.7 19.8 + - + +
8U GLU* 1.3 71.3 - - - +
10U VAL* 1.3 66.0 + - - +
12U GLU* 3.2 9.8 + - + +
13U LEU* 3.1 42.4 + - + +
28U ALA* 4.4 16.6 - - + +
31U LEU* 3.6 36.8 - - + -
32U ARG* 5.2 2.7 - - + +
70U LEU* 4.5 16.2 - - + -
73U LEU* 5.3 6.5 - - + +
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Residues in contact with VAL 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6U PRO 3.0 19.2 + - - +
7U ARG* 4.0 8.7 - - - +
9U ILE* 1.3 75.4 - - - +
11U SER* 1.3 57.9 + - - +
13U LEU* 2.6 34.2 + - - +
14U ASP* 3.0 30.2 + - - +
24U LYS* 4.7 14.1 - - + -
25U ARG* 5.0 13.7 - - + +
28U ALA* 4.8 9.4 - - + -
409V PHE* 4.5 19.5 - - + -
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Residues in contact with SER 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U ARG 3.8 11.3 + - - -
8U GLU* 3.0 11.7 + - - -
10U VAL* 1.3 77.4 - - - +
12U GLU* 1.3 58.6 + - - +
14U ASP* 3.7 23.7 + - - +
15U GLN* 4.0 12.8 - - - +
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Residues in contact with GLU 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U MET* 4.3 21.6 - - - +
8U GLU 3.0 10.1 + - - +
9U ILE* 3.6 12.8 - - + +
10U VAL 2.9 1.6 + - - -
11U SER* 1.3 76.7 - - - +
13U LEU* 1.3 62.3 + - + +
15U GLN* 4.0 17.0 + - - +
16U HIS* 3.9 15.9 + - + -
73U LEU* 3.0 47.2 - - + +
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Residues in contact with LEU 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U ILE* 3.1 32.1 - - + +
10U VAL* 2.6 12.2 + - - +
12U GLU* 1.3 74.6 - - + +
14U ASP* 1.3 55.0 + - - +
15U GLN 2.7 16.9 + - - -
16U HIS* 3.1 5.5 + - - +
17U ILE* 3.1 32.3 + - + +
24U LYS* 4.3 33.4 - - + +
27U VAL* 5.0 2.9 - - + -
28U ALA* 6.0 0.7 - - + +
66U ILE* 4.7 15.3 - - + +
69U ARG* 3.0 43.1 - - + +
70U LEU* 5.0 7.0 - - + -
73U LEU* 4.5 7.4 - - + -
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Residues in contact with ASP 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U VAL* 3.0 26.8 + - - +
11U SER* 3.8 16.8 + - - +
12U GLU 3.4 0.8 - - - -
13U LEU* 1.3 73.9 - - - +
15U GLN* 1.3 60.6 + - + +
16U HIS 3.6 0.9 - - - -
17U ILE 4.5 5.2 - - - -
18U ILE* 4.6 21.1 - - + +
24U LYS* 2.8 35.0 + - - +
347U GLU* 5.6 2.9 - - - +
348U PRO* 5.4 2.1 - - - +
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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
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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