Contacts of the strand formed by residues 129 - 136 (chain E) in PDB entry 5GJQ
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 ILE 129 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 3.6 4.2 - - - +
71E MET* 5.1 5.2 - - + -
73E PHE* 5.0 8.1 - - + -
74E ALA 3.3 9.4 - - - +
75E GLY* 4.1 3.1 - - - +
76E LEU 3.2 32.1 - - - +
79E ASP* 3.8 4.3 - - + -
80E ALA* 3.6 34.1 - - + +
83E VAL* 4.0 24.5 - - + -
115E LYS* 3.5 24.6 + - - +
127E PHE* 3.0 15.1 + - + +
128E GLY* 1.3 84.3 - - - +
130E SER* 1.3 63.7 + - - +
131E ALA* 5.3 0.2 - - + -
149E PRO* 3.3 18.7 - - - +
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Residues in contact with SER 130 (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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23E GLN* 5.7 0.2 - - - +
26E VAL* 3.4 22.8 - - - +
73E PHE* 3.2 5.2 - - - +
74E ALA 2.9 32.1 + - - -
115E LYS* 4.0 4.5 - - - +
129E ILE* 1.3 71.7 - - - +
131E ALA* 1.3 62.6 + - - +
146E GLN* 5.1 1.0 + - - -
147E THR 3.7 12.8 + - - -
148E ASP* 4.1 4.3 + - - -
149E PRO* 3.3 21.1 - - - +
161E ILE* 3.7 21.1 - - - +
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Residues in contact with ALA 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E MET* 3.8 22.0 - - + -
72E ALA 3.4 10.5 - - - +
73E PHE* 4.3 0.9 - - + +
111E ILE* 5.4 2.7 - - + -
115E LYS* 4.1 6.3 - - - +
129E ILE* 5.3 1.6 - - + -
130E SER* 1.3 78.0 - - - +
132E LEU* 1.3 64.3 + - - +
133E ILE* 3.8 13.2 + - + -
146E GLN* 3.4 10.0 - - - +
147E THR* 3.2 41.4 + - - +
161E ILE* 4.2 2.2 - - - -
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Residues in contact with LEU 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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32E ALA* 3.7 20.9 - - + +
33E VAL* 3.6 33.2 - - - +
34E GLY* 3.7 5.6 - - - +
43E LEU* 4.3 6.9 - - + +
71E MET* 3.3 3.5 - - - -
72E ALA* 2.9 46.3 + - + +
131E ALA* 1.3 71.8 - - - +
133E ILE* 1.3 63.1 + - - +
134E VAL* 3.8 0.8 + - + -
144E LEU* 3.7 29.2 - - + -
145E TYR 3.6 1.1 - - - -
146E GLN* 3.9 26.5 - - + +
159E ASN* 4.2 12.3 - - + +
160E ALA* 4.7 0.7 - - - -
161E ILE* 3.8 17.0 - - + +
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Residues in contact with ILE 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LEU* 4.7 2.2 - - + -
69E VAL* 3.8 16.2 - - + -
70E CYS 3.9 4.0 - - - +
71E MET* 4.3 8.3 - - + -
104E VAL* 3.7 21.7 - - + +
107E ILE* 4.2 6.1 - - + -
108E THR* 3.4 46.2 - - + +
111E ILE* 3.6 24.7 - - + -
131E ALA* 3.8 12.1 - - + +
132E LEU* 1.3 75.1 - - - +
134E VAL* 1.3 59.9 + - - +
143E ARG 4.1 0.3 - - - +
144E LEU* 3.3 5.2 - - - +
145E TYR* 2.8 36.5 + - + +
147E THR* 4.2 12.3 - - + -
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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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34E GLY* 5.8 1.1 - - - -
35E VAL 6.2 0.2 - - - +
41E VAL* 3.6 32.8 - - + -
42E VAL 5.5 2.0 - - - +
43E LEU* 3.6 44.4 - - + -
69E VAL* 3.5 2.6 - - - +
70E CYS* 2.9 43.8 + - - +
104E VAL* 4.1 4.7 - - - -
132E LEU* 3.8 2.0 + - + +
133E ILE* 1.3 72.7 - - - +
135E GLY* 1.3 62.7 + - - +
143E ARG 3.4 5.2 - - - +
144E LEU* 3.5 32.8 - - + -
211E MET* 4.9 0.2 - - + -
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Residues in contact with GLY 135 (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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41E VAL* 4.6 8.8 - - - +
68E ASN 3.6 13.0 - - - -
69E VAL* 4.4 0.2 - - - -
104E VAL* 3.7 17.7 - - - +
134E VAL* 1.3 79.6 - - - +
136E PHE* 1.3 61.4 + - - +
142E PRO* 3.7 2.3 - - - +
143E ARG* 2.8 35.0 + - - +
211E MET* 5.1 3.6 - - - -
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Residues in contact with PHE 136 (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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41E VAL* 5.7 3.8 - - + -
68E ASN* 2.8 35.0 + - - +
135E GLY* 1.3 74.8 - - - +
137E ASP* 1.3 65.6 + - - +
140E GLY* 5.3 4.7 - - - +
141E THR 3.9 8.1 - - - +
142E PRO* 4.5 6.3 - - + -
211E MET* 5.0 5.9 - - + +
212E ARG 5.6 1.3 - - - +
213E ARG* 4.3 26.7 - - - +
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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