Contacts of the strand formed by residues 80 - 88 (chain A) in PDB entry 1VJZ
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 HIS 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A TRP* 3.6 33.5 + + - +
39A ASN 2.7 17.7 + - - +
40A PHE* 3.5 24.2 - + + -
41A VAL 2.9 27.4 + - - +
78A GLY 4.1 0.6 - - - -
79A ILE* 1.3 73.4 - - - +
81A ILE* 1.3 69.0 + - - +
129A SER 3.3 21.7 + - - -
130A THR 3.1 25.0 + - - +
131A HIS* 3.6 5.6 - - - +
132A LEU 3.5 13.2 - - - -
133A SER* 2.7 31.2 + - - -
172A LEU* 4.6 0.2 - - + -
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Residues in contact with ILE 81 (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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30A PHE* 3.8 12.3 - - + -
41A VAL* 3.5 25.1 - - + -
43A ILE* 4.0 13.7 - - + -
70A VAL* 3.7 28.3 - - + +
71A ILE* 4.1 15.5 - - + +
74A GLY* 3.9 14.4 - - - -
79A ILE* 3.8 8.1 - - + +
80A HIS* 1.3 76.9 + - - +
82A CYS* 1.3 61.7 + - - +
83A ILE* 3.8 25.4 - - + -
131A HIS 2.8 17.6 + - - +
132A LEU* 3.2 11.8 - - + +
133A SER 2.9 23.7 + - - -
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Residues in contact with CYS 82 (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* 3.5 29.6 - - + -
41A VAL 2.8 10.4 + - - +
42A ARG* 3.3 12.5 - - - +
43A ILE 2.9 25.8 + - - -
80A HIS* 3.8 0.6 - - - -
81A ILE* 1.3 73.4 - - - +
83A ILE* 1.3 61.4 + - - +
84A SER 3.8 0.2 + - - -
133A SER* 3.5 20.2 - - - +
135A ASN* 3.5 33.0 - - - -
174A ILE* 3.8 13.9 - - - -
256A PHE* 6.0 0.4 - - - -
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Residues in contact with ILE 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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43A ILE* 3.8 14.4 - - + -
45A MSE 4.1 17.9 - - + -
64A PHE* 5.8 0.4 - - + -
67A ILE* 4.1 20.4 - - + -
70A VAL* 5.6 0.7 - - + -
71A ILE* 4.7 1.6 - - + -
81A ILE* 3.8 23.1 - - + -
82A CYS* 1.3 72.4 - - - +
84A SER* 1.3 59.0 + - - +
117A TRP* 3.7 7.7 - - + -
120A ILE* 3.6 31.4 - - + -
124A TYR* 4.2 14.8 - - + -
132A LEU* 4.0 8.7 - - + -
133A SER 3.1 13.4 + - - +
134A PHE* 3.6 15.8 - - + -
135A ASN 2.8 23.2 + - - -
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Residues in contact with SER 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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42A ARG* 3.4 22.5 + - - -
43A ILE 2.9 15.2 + - - +
44A PRO* 3.9 7.0 - - - +
45A MSE 2.7 38.3 + - - +
83A ILE* 1.3 76.6 - - - +
85A LEU* 1.3 68.9 + - - +
86A HIS 4.2 0.5 + - - -
117A TRP* 4.6 0.7 - - - -
135A ASN* 2.9 34.2 + - - -
138A ASN* 4.4 2.1 + - - +
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Residues in contact with LEU 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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45A MSE 3.6 15.0 - - + +
47A HIS* 5.2 2.0 - - + -
50A TRP* 3.7 34.3 - - + -
84A SER* 1.3 73.1 + - - +
86A HIS* 1.3 62.2 + - - +
87A ARG 3.9 11.9 - - - +
88A ALA* 3.7 27.4 - - + -
89A PRO* 5.3 0.7 - - + -
113A PHE* 4.1 6.1 - - + -
116A HIS* 4.7 15.7 - - + -
117A TRP* 3.5 34.5 - - + +
120A ILE* 4.6 3.6 - - + -
135A ASN 3.3 7.9 + - - -
136A LEU 3.5 8.5 - - - +
137A ILE* 3.4 4.7 - - + +
138A ASN 2.8 25.6 + - - -
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Residues in contact with HIS 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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17A PHE* 3.4 40.0 + + + +
44A PRO* 3.8 30.1 - - + +
45A MSE 2.7 17.5 + - - +
84A SER 3.5 3.2 + - - -
85A LEU* 1.3 73.0 - - - +
87A ARG* 1.3 55.9 + - - +
91A TYR 4.0 0.7 - - - +
92A SER* 2.9 26.4 + - - -
93A VAL* 3.6 26.4 + - + +
94A ASN* 4.0 13.0 - - + +
137A ILE* 4.8 2.1 - - - +
138A ASN* 3.2 42.2 + - + +
139A GLU* 4.7 1.2 + - - -
259A GLU* 4.7 1.0 + - - -
292A TRP* 4.3 9.8 - + - -
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Residues in contact with ARG 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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17A PHE 5.9 0.7 - - - +
19A ILE* 4.9 0.2 - - - +
45A MSE 3.1 8.2 + - - +
46A CYS* 4.1 23.3 - - - -
47A HIS* 3.1 37.4 + - + +
48A LEU* 3.6 25.2 - - - +
85A LEU* 3.9 6.6 - - - +
86A HIS* 1.3 78.3 - - - +
88A ALA* 1.3 64.3 + - - +
91A TYR 3.5 3.1 - - - -
92A SER* 3.5 25.0 + - - +
94A ASN* 2.9 33.7 + - + +
96A GLU* 3.9 8.1 + - - +
97A VAL* 3.0 40.0 + - - +
99A GLU* 2.8 43.8 + - - +
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Residues in contact with ALA 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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47A HIS* 3.5 13.7 - - - -
85A LEU* 3.7 13.7 - - + -
87A ARG* 1.3 76.2 - - - +
89A PRO* 1.3 80.3 - - + +
90A GLY 3.0 1.2 + - - -
91A TYR 2.9 19.9 + - - +
99A GLU* 3.9 1.0 - - - -
103A LEU* 4.7 2.0 - - + -
113A PHE* 3.5 25.8 - - + -
137A ILE* 3.7 15.9 - - + +
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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