Contacts of the strand formed by residues 130 - 134 (chain E) in PDB entry 1GEC
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 VAL 130 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E THR* 3.5 4.9 - - - -
113E VAL* 4.1 7.0 - - + -
121E LEU* 4.3 2.5 - - + -
124E ALA* 3.7 30.3 - - + +
125E ILE* 4.0 14.8 - - + +
128E GLN* 3.5 15.7 - - + +
129E PRO* 1.3 71.9 - - - +
131E SER* 1.3 71.8 + - - +
132E VAL* 3.8 7.9 - - + -
162E THR* 3.3 6.4 - - - +
163E ALA* 2.8 32.7 + - + -
210E SER* 3.7 20.4 - - - -
211E TYR 3.2 16.6 - - - +
212E TYR* 4.5 7.0 - - + -
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Residues in contact with SER 131 (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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29E SER* 3.7 22.3 + - - -
30E THR* 4.6 3.5 - - - +
33E THR* 3.4 18.2 - - - +
68E GLN* 3.3 26.4 + - - +
72E LEU* 4.8 6.1 - - - -
130E VAL* 1.3 70.4 - - - +
132E VAL* 1.3 60.5 + - - +
160E ALA* 4.5 0.2 - - - +
161E VAL 3.5 5.4 - - - -
210E SER* 3.1 7.3 - - - -
211E TYR* 2.8 44.9 + - - -
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Residues in contact with VAL 132 (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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68E GLN* 4.1 2.2 - - - -
121E LEU* 4.2 10.3 - - + -
130E VAL* 3.7 8.3 + - + -
131E SER* 1.3 77.3 - - - +
133E VAL* 1.3 73.1 + - - +
160E ALA* 3.2 5.7 - - - +
161E VAL* 2.7 47.8 + - + +
163E ALA* 3.9 27.1 - - + -
177E ILE* 4.8 1.3 - - + -
206E VAL* 3.1 45.8 - - + +
209E SER 3.9 5.4 - - - -
210E SER* 3.5 18.2 - - - +
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Residues in contact with VAL 133 (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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68E GLN* 4.6 7.2 - - - +
132E VAL* 1.3 90.8 - - + +
134E VAL* 1.3 62.3 + - - +
157E VAL* 3.5 38.6 - - + -
159E HIS 3.1 14.8 - - - +
160E ALA* 4.8 1.6 - - - +
205E GLY 3.8 5.2 - - - +
206E VAL* 3.3 13.2 - - - -
208E ARG* 3.9 2.9 - - + +
209E SER* 3.6 36.3 + - - +
1I PHQ 4.6 5.4 - - + -
3I VAL* 3.8 21.1 - - + -
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Residues in contact with VAL 134 (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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133E VAL* 1.3 80.6 - - - +
135E GLU* 1.3 63.0 + - - +
141E PHE* 4.1 16.4 - - + -
157E VAL* 3.7 6.1 - - - -
158E ASP* 3.0 17.8 + - - +
159E HIS* 2.8 41.2 + - + +
161E VAL* 3.9 23.6 - - + -
177E ILE* 4.5 0.2 - - + -
193E ILE* 3.8 29.8 - - + -
204E CYS* 3.5 12.1 - - + +
206E VAL* 3.9 15.5 - - + -
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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