Contacts of the strand formed by residues 95 - 99 (chain E) in PDB entry 1GMO
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 95 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E THR* 3.8 24.6 + - - +
62E LYS* 3.8 12.3 - - - +
63E LYS* 3.9 8.5 - - + +
64E VAL 4.4 0.4 - - - +
89E PHE* 3.6 7.1 - - - -
90E ASP* 3.0 29.5 + - + +
93E ARG* 3.0 52.1 + - + +
94E LYS* 1.3 77.5 - - - +
96E CYS* 1.3 72.4 + - - +
97E LEU* 3.5 21.5 - - + +
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Residues in contact with CYS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E THR* 3.4 14.5 - - - -
62E LYS 3.2 8.9 + - - +
64E VAL* 3.7 24.9 - - - -
70E CYS* 2.0 54.1 - - + -
88E VAL 3.4 5.8 - - - -
95E GLN* 1.3 79.3 - - - +
97E LEU* 1.3 72.7 + - - +
98E TRP* 3.6 31.6 - - + -
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E THR* 4.9 7.0 - - - +
50E LEU 5.8 1.1 - - - +
59E ILE* 5.8 0.9 - - + -
60E LYS 3.6 6.3 - - - -
61E THR* 3.9 12.8 - - + -
87E PHE* 3.2 1.7 - - - +
88E VAL* 2.9 36.1 + - + +
90E ASP* 4.6 7.6 - - + +
93E ARG* 6.2 0.2 - - - +
95E GLN* 3.5 33.0 - - + +
96E CYS* 1.3 96.2 - - - +
98E TRP* 1.3 62.2 + - - +
99E PHE* 2.9 47.3 - - + -
116E PHE* 5.5 6.3 - - + -
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Residues in contact with TRP 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ILE* 3.6 1.4 - - - +
60E LYS* 3.2 39.7 + - + +
61E THR* 3.9 8.7 - - - -
62E LYS* 3.9 26.0 - - + -
64E VAL* 5.1 3.6 - - + -
69E GLN 4.4 1.1 - - - -
70E CYS* 2.9 29.2 + - - +
73E ARG* 3.5 44.6 - - + -
74E CYS* 3.8 5.9 - - + +
80E LEU* 3.9 33.7 - - + -
82E PHE* 3.4 11.0 - - + -
84E CYS* 3.6 18.2 - - - -
86E ALA 3.7 2.9 - - - -
87E PHE* 3.5 18.6 - - + -
96E CYS* 3.6 31.6 - - + -
97E LEU* 1.3 71.5 - - - +
99E PHE* 1.3 64.6 + - - +
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Residues in contact with PHE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E THR* 4.9 0.2 - - - -
50E LEU* 4.3 21.8 - - + -
59E ILE* 3.9 26.0 - - + -
82E PHE* 3.8 4.3 - - - -
83E THR 3.8 0.7 - - - +
84E CYS* 3.8 1.6 - - - -
85E LYS 3.1 20.6 + - - -
86E ALA* 2.9 25.5 + - + +
87E PHE 4.3 0.2 - - - -
88E VAL* 3.3 28.7 - - + -
97E LEU* 2.9 51.8 - - + -
98E TRP* 1.3 78.1 - - - +
100E PRO* 1.3 64.0 - - - +
101E PHE* 3.0 52.9 + + + +
102E ASN* 6.2 0.2 - - - -
118E LEU* 5.1 1.6 - - + -
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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