Contacts of the strand formed by residues 82 - 88 (chain A) in PDB entry 1JEQ
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 LEU 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 4.4 21.8 - - + +
36A ASP 2.8 10.5 + - - +
37A SER* 3.3 19.5 - - - +
38A LEU* 2.8 25.8 + - - +
80A ARG 4.4 1.8 - - - +
81A ASP* 1.3 73.7 - - - +
83A LEU* 1.3 65.1 + - - +
108A LEU* 3.8 13.2 - - + +
109A ASP* 3.4 29.4 - - - +
110A ASN* 3.4 24.7 - - - +
157A VAL* 3.8 29.8 - - + -
159A PHE* 4.3 17.0 - - + -
161A MET* 5.3 1.3 - - + -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.3 26.5 - - + +
40A PHE* 3.9 13.9 - - + -
70A VAL* 4.6 0.9 - - + +
71A TYR* 3.6 56.3 - - + +
74A LYS* 4.1 26.5 - - + -
81A ASP* 4.6 8.1 - - + +
82A LEU* 1.3 84.4 - - - +
84A ALA* 1.3 60.9 + - - +
107A GLU 3.2 0.3 - - - +
108A LEU* 3.9 2.9 - - - -
109A ASP 2.8 20.4 + - - +
111A PRO* 4.2 15.3 - - + -
115A ARG* 3.0 23.0 + - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU 3.0 5.7 + - - -
39A ILE* 3.8 28.9 - - + -
40A PHE* 2.9 32.9 + - - -
71A TYR* 3.8 1.6 - - - -
83A LEU* 1.3 74.3 - - - +
85A VAL* 1.3 65.4 + - - +
106A GLN 3.3 15.7 - - - +
107A GLU* 3.8 1.1 - - - -
108A LEU* 3.6 19.1 - - + +
153A LEU* 4.5 6.1 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.7 6.5 - - + +
42A VAL* 5.9 0.2 - - + -
67A ILE* 4.5 8.3 - - + -
71A TYR* 2.9 31.6 - - + +
84A ALA* 1.3 74.9 - - - +
86A VAL* 1.3 65.5 + - - +
87A PHE* 3.4 35.2 - - + -
105A LEU* 3.0 32.8 + - + -
106A GLN* 2.8 31.5 + - + +
119A LEU* 3.9 17.3 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE* 3.8 14.6 - - + -
40A PHE 2.8 12.1 + - - +
41A LEU* 3.2 26.0 - - + +
42A VAL 2.7 30.8 + - - -
85A VAL* 1.3 81.9 - - - +
87A PHE* 1.3 65.8 + - - +
102A ILE* 4.2 17.0 - - + -
103A TYR 3.7 9.6 - - - +
104A VAL* 4.2 11.9 - - + -
146A VAL* 5.5 0.2 - - + -
149A VAL* 5.1 1.1 - - + -
150A CYS* 4.4 7.2 - - - -
153A LEU* 3.5 31.9 - - + -
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.3 44.9 - - + +
44A ALA* 4.7 1.1 - - + -
60A PHE* 4.1 1.6 - + - -
64A ILE* 3.9 26.7 - - + -
85A VAL* 3.4 31.6 - - + -
86A VAL* 1.3 79.1 - - - +
88A TYR* 1.3 61.1 + - - +
90A THR* 3.8 20.0 - - + -
102A ILE* 3.7 1.7 - - - -
103A TYR* 2.9 40.7 + - + +
105A LEU* 3.8 22.9 - - + -
119A LEU* 4.6 1.1 - - + -
122A PHE* 4.6 4.3 - + - -
131A PHE* 3.8 31.2 - + + -
135A MET* 4.5 6.3 - - + -
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.8 21.5 - - + -
42A VAL 3.2 9.0 + - - -
43A ASP* 3.0 47.1 + - + +
44A ALA* 3.0 27.0 + - - +
87A PHE* 1.3 75.2 - - - +
89A GLY* 1.3 66.7 + - - +
90A THR* 3.1 3.1 - - - -
101A ASN 3.5 7.6 - - - +
102A ILE* 4.4 2.7 - - + +
141A TYR* 3.6 42.5 + + - -
143A LEU* 4.1 10.4 - - + +
146A VAL* 3.5 30.5 - - + -
168A LEU* 3.7 20.9 - - + +
170A THR* 3.5 11.3 + - - -
175A PRO* 5.6 0.2 - - - +
217A TYR* 4.2 9.2 + - - -
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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