Contacts of the strand formed by residues 136 - 141 (chain B) in PDB entry 1J3R
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 ALA 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B HIS 3.5 10.8 - - - +
90B TYR* 3.3 44.3 - - + +
111B LEU* 3.2 6.2 - - - +
112B GLN* 2.7 32.1 + - + +
135B TRP* 1.3 77.6 - - - +
137B HIS* 1.3 60.6 + - - +
164B ILE* 4.1 6.5 - - + -
169B PHE* 4.1 15.9 - - + -
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 3.3 16.6 - - - -
89B HIS* 3.3 40.5 + + - -
91B HIS* 4.3 7.6 - + - -
98B GLU* 3.0 25.4 + - - -
100B TYR* 2.7 39.2 + + - -
109B MET* 3.7 24.0 - - + -
110B LEU 3.3 6.7 - - - +
111B LEU* 4.1 7.6 - - + -
131B VAL* 3.9 15.3 - - + +
135B TRP 4.0 3.0 + - - -
136B ALA* 1.3 79.9 - - - +
138B ARG* 1.3 63.5 + - - +
139B THR* 5.4 0.4 - - - -
169B PHE* 3.9 3.8 - - - -
601B 6PG 4.3 2.9 + - - -
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 3.7 16.2 + - - +
82B GLU* 5.6 1.8 + - - -
85B MET* 3.2 41.6 - - - +
86B THR* 2.6 33.3 + - - +
87B LYS 3.3 17.4 + - - -
88B GLY* 3.8 3.1 - - - -
109B MET* 3.3 5.0 - - - +
110B LEU* 2.8 41.3 + - + +
137B HIS* 1.3 77.1 - - - +
139B THR* 1.3 66.8 + - - +
140B ILE* 3.8 17.0 + - + +
164B ILE* 4.9 1.8 - - - +
168B GLY* 5.7 0.4 - - - -
169B PHE* 3.1 52.9 - - + +
171B LYS 4.4 7.3 + - - -
172B ILE* 5.9 3.0 - - - +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 3.5 5.9 - - + +
85B MET* 3.2 5.7 - - - +
86B THR* 2.9 40.4 + - - -
100B TYR* 3.7 17.8 + - - -
108B GLY 3.7 2.7 - - - -
109B MET* 4.1 7.8 - - - +
123B MET* 3.8 6.4 - - + +
137B HIS* 5.4 0.5 - - - -
138B ARG* 1.3 74.9 - - - +
140B ILE* 1.3 64.5 + - - +
147B PHE* 3.3 23.8 - - + -
149B PHE* 3.1 43.4 - - + -
601B 6PG 5.0 0.5 + - - -
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.5 4.9 - - - -
83B PHE* 3.4 29.2 - - + +
84B PHE 3.6 4.5 - - - +
85B MET* 3.2 37.2 - - + -
107B GLY* 3.1 5.2 - - - -
108B GLY 2.8 40.8 + - - +
110B LEU* 4.9 4.9 - - + -
120B PHE* 4.4 7.9 - - + -
138B ARG* 3.8 17.7 - - + +
139B THR* 1.3 77.6 - - - +
141B ASN* 1.3 65.1 + - - +
142B THR* 3.8 2.7 - - + -
147B PHE* 3.6 4.2 - - - -
173B VAL* 3.9 39.0 - - + +
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Residues in contact with ASN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 2.7 43.8 + - + +
75B TYR 4.0 5.6 - - - +
76B PRO* 3.4 14.8 - - + -
77B GLY 4.6 1.9 + - - +
83B PHE* 3.3 23.4 - - - +
84B PHE* 3.1 13.0 + - + +
106B LYS 3.4 6.8 - - - +
140B ILE* 1.3 70.1 - - - +
142B THR* 1.3 59.8 + - - +
143B GLY* 2.7 42.1 + - - +
145B LYS 3.0 21.1 + - - +
147B PHE* 3.3 12.3 - - + +
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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