Contacts of the strand formed by residues 130 - 138 (chain m) 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 VAL 130 (chain m).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29m VAL* 4.4 1.1 - - - -
74m ILE* 4.5 0.2 - - + -
75m ALA 3.6 18.6 - - - +
76m GLY 4.3 0.2 - - - +
77m LEU 3.9 9.6 - - - +
80m ASP* 3.8 23.6 - - + -
81m ALA* 3.8 24.5 - - + +
84m LEU* 3.9 27.4 - - + +
128m TYR* 3.0 13.3 + - + +
129m GLY* 1.3 77.7 - - - +
131m GLY* 1.3 73.9 + - - +
132m LEU* 4.2 6.6 - - + +
147m THR* 4.5 3.3 + - - +
148m CYS 4.4 1.6 - - - -
149m PRO* 3.8 20.2 - - - +
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Residues in contact with GLY 131 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29m VAL* 3.9 13.4 - - - +
74m ILE* 3.7 0.3 - - - -
75m ALA* 2.9 37.6 + - - -
130m VAL* 1.3 76.3 - - - +
132m LEU* 1.3 67.6 + - - +
147m THR* 3.1 14.4 - - - -
149m PRO* 4.6 0.7 - - - -
161m ILE* 3.8 11.7 - - - +
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Residues in contact with LEU 132 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72m ILE* 4.2 11.4 - - + -
73m SER 3.5 4.9 - - - +
74m ILE* 3.7 27.8 - - + -
81m ALA* 5.1 3.6 - - + +
84m LEU* 3.9 28.5 - - + -
88m MET* 4.2 24.0 - - - -
112m ILE* 4.3 12.1 - - + -
130m VAL* 4.2 9.6 - - + +
131m GLY* 1.3 86.4 - - - +
133m LEU* 1.3 64.6 + - - +
134m ILE* 4.1 13.0 - - + -
146m GLN* 3.3 8.0 - - - +
147m THR* 2.9 48.1 + - - +
161m ILE* 4.1 2.8 - - - +
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Residues in contact with LEU 133 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35m THR* 3.8 37.5 - - + +
36m VAL* 3.9 20.9 - - - +
37m GLY* 4.0 4.9 - - - +
46m LEU* 3.9 17.0 - - + +
72m ILE* 3.2 5.4 - - - -
73m SER* 2.8 36.3 + - - +
132m LEU* 1.3 79.7 - - - +
134m ILE* 1.3 61.9 + - - +
144m ILE* 4.9 4.3 - - + -
145m PHE 3.3 11.2 - - - +
146m GLN* 4.1 10.3 - - + -
159m MET* 4.1 27.4 - - + +
160m SER* 4.5 0.9 - - - -
161m ILE* 4.0 14.6 - - + -
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Residues in contact with ILE 134 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70m ILE* 4.2 12.1 - - + -
71m GLY 3.7 8.1 - - - +
72m ILE* 4.1 14.1 - - + -
88m MET* 4.2 5.4 - - + -
105m VAL* 4.0 23.5 - - + +
108m LEU* 5.3 1.8 - - + -
109m VAL* 3.8 21.1 - - + -
112m ILE* 3.8 27.1 - - + -
132m LEU* 4.3 9.0 - - + +
133m LEU* 1.3 77.7 - - - +
135m ALA* 1.3 62.4 + - - +
136m GLY 4.1 0.4 + - - -
143m HIS 3.3 2.6 - - - +
144m ILE* 3.3 8.8 - - - +
145m PHE* 2.9 45.1 + - + +
147m THR* 4.0 17.0 - - + -
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Residues in contact with ALA 135 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44m ALA* 4.2 12.6 - - + -
46m LEU* 3.5 35.2 - - + +
70m ILE* 3.6 2.3 - - - +
71m GLY 2.9 33.1 + - - +
133m LEU 4.1 0.4 + - - -
134m ILE* 1.3 75.2 - - - +
136m GLY* 1.3 59.2 + - - +
143m HIS 3.3 4.7 - - - +
144m ILE* 3.8 11.2 - - + -
215m VAL* 4.0 7.5 - - + +
221m PHE* 4.3 7.7 - - + -
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Residues in contact with GLY 136 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44m ALA* 4.0 3.9 - - - +
69m HIS 3.2 11.7 - - - -
70m ILE* 4.5 2.0 - - - -
105m VAL* 4.1 17.7 - - - +
134m ILE 4.1 0.4 + - - -
135m ALA* 1.3 77.3 - - - +
137m TYR* 1.3 63.2 + - - +
141m GLY 4.6 0.2 - - - -
142m PRO* 3.4 3.6 - - - +
143m HIS* 2.9 33.5 + - - +
215m VAL* 3.7 7.4 - - - +
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Residues in contact with TYR 137 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41m LYS 5.0 1.6 + - - -
42m THR* 3.6 22.7 - - - -
69m HIS* 3.1 32.3 + - + +
105m VAL* 4.1 4.2 - - - +
136m GLY* 1.3 73.4 - - - +
138m ASP* 1.3 80.3 + - - +
141m GLY* 3.4 31.5 - - - -
142m PRO* 3.4 16.6 - - + -
215m VAL* 4.3 19.3 - - + -
216m GLY* 4.1 16.6 - - - +
217m LYS* 3.4 29.6 - - + +
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Residues in contact with ASP 138 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69m HIS* 5.2 3.4 - - + -
104m PRO* 4.5 11.2 - - + -
105m VAL* 3.3 32.1 + - + +
106m SER* 4.6 2.1 + - - -
137m TYR* 1.3 93.7 + - - +
139m ASP* 1.3 64.3 + - - +
140m MET* 2.8 28.1 + - - -
141m GLY 2.9 19.6 + - - -
143m HIS* 3.2 24.3 + - - -
81u HIS* 3.4 20.4 + - - +
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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