Contacts of the strand formed by residues 4 - 11 (chain G) in PDB entry 1GLE
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 LYS 4 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G TYR* 1.4 86.6 + - - +
22G ASP* 4.5 0.7 - - - +
23G HIS* 3.8 10.0 + - + +
71G SER 5.5 0.4 + - - -
72G ASP 3.4 18.2 + - - +
73G GLN* 3.1 41.6 - - + +
74G ILE 4.3 10.5 + - - -
75G ALA* 4.4 11.2 - - + +
453G PHE* 3.5 27.6 - - + -
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Residues in contact with TYR 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LYS* 1.4 93.5 + - - +
6G ILE* 1.3 63.7 + - - +
7G VAL* 5.3 0.2 - - + -
20G VAL* 4.1 14.4 - - + -
21G MET 2.8 24.0 - - - +
22G ASP* 4.0 15.3 - - + -
28G ILE* 5.2 9.9 - - + -
68G ASP 5.1 0.3 + - - -
69G ILE* 3.3 41.5 - - + +
73G GLN* 2.9 44.7 + - + -
74G ILE* 3.0 17.8 - - + +
75G ALA 2.8 24.2 + - - -
453G PHE* 3.8 8.0 - - - -
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Residues in contact with ILE 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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5G TYR* 1.3 73.9 - - - +
7G VAL* 1.3 67.4 + - - +
20G VAL* 3.6 0.9 - - - +
21G MET* 2.9 48.5 + - + +
22G ASP 4.3 0.2 - - - +
75G ALA* 4.6 2.2 - - + -
76G ALA* 3.2 37.2 - - + +
444G ALA* 4.2 11.2 - - + +
447G ALA* 3.9 21.8 - - + -
448G GLY* 4.0 6.3 - - - +
453G PHE* 3.6 22.4 - - + -
454G TRP* 3.0 43.3 - - + -
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Residues in contact with VAL 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G TYR 4.7 0.4 - - - +
6G ILE* 1.3 82.0 - - - +
8G ALA* 1.3 61.8 + - - +
9G LEU* 3.9 7.2 - - + -
19G VAL 3.2 5.4 - - - +
20G VAL* 3.1 36.1 - - + -
60G LEU* 3.8 29.4 - - + -
64G LEU* 4.4 6.1 - - + -
74G ILE* 4.3 18.6 - - + -
76G ALA 3.1 8.9 + - - +
77G ILE* 3.3 19.7 - - + +
78G GLY* 2.8 25.4 + - - +
444G ALA* 5.6 1.1 - - - -
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Residues in contact with ALA 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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6G ILE 4.3 0.4 - - - -
7G VAL* 1.3 73.4 - - - +
9G LEU* 1.3 78.4 + - - +
10G ASP 4.1 0.3 + - - -
18G ALA* 3.4 1.4 - - - -
19G VAL* 2.8 34.6 + - + +
21G MET* 4.2 15.1 - - + +
78G GLY 3.3 5.4 - - - +
440G ALA* 3.8 32.1 - - + +
443G ALA* 4.1 9.6 - - + -
444G ALA* 4.3 5.2 - - + +
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Residues in contact with LEU 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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7G VAL* 3.9 8.3 - - + +
8G ALA* 1.3 102.3 - - - +
10G ASP* 1.3 57.4 + - - +
11G GLN 3.9 0.4 - - - -
17G ARG 4.0 1.1 - - - -
18G ALA* 4.2 5.6 - - + -
56G GLN* 3.7 30.1 - - + +
60G LEU* 3.4 46.4 - - + -
77G ILE* 4.8 6.1 - - + -
78G GLY 2.8 14.0 + - - +
79G ILE* 4.1 19.3 - - + -
80G THR* 2.5 39.4 + - - +
169G LEU* 5.2 4.7 - - + -
173G MET* 4.3 17.5 - - + -
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Residues in contact with ASP 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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8G ALA 4.1 1.0 + - - -
9G LEU* 1.3 72.3 - - - +
11G GLN* 1.3 66.5 + - - +
12G GLY 3.6 3.1 + - - -
15G SER 3.8 1.0 - - - +
16G SER* 3.6 0.7 - - - -
17G ARG* 2.8 64.6 + - + +
19G VAL* 6.1 0.6 - - - +
56G GLN* 3.4 2.5 - - - -
80G THR* 3.3 12.0 - - - +
245G ASP* 4.1 5.0 - - - +
439G THR* 3.1 28.5 - - - +
440G ALA* 4.2 10.2 + - + -
502G ZN 3.1 30.3 - - - -
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Residues in contact with GLN 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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9G LEU 3.9 0.2 - - - -
10G ASP* 1.3 72.2 - - - +
12G GLY* 1.3 77.7 + - - +
15G SER 4.1 0.7 - - - -
16G SER* 2.9 20.6 + - - +
35G PHE* 3.4 14.1 - - - -
52G ILE* 3.0 27.3 - - + +
56G GLN* 2.8 27.3 - - + +
80G THR 2.6 12.4 + - - +
81G ASN* 3.3 1.2 - - - -
82G GLN* 2.9 42.3 + - - +
165G VAL* 3.1 22.3 - - + +
169G LEU* 3.8 14.6 - - + -
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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