Contacts of the strand formed by residues 117 - 128 (chain A) in PDB entry 1VLM
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLU* 3.4 9.7 - - - +
91A PHE 3.5 11.2 - - - +
92A ASP 4.0 3.4 - - - +
93A PHE* 3.6 25.6 - - - +
94A ALA* 3.7 7.6 - - + +
113A ALA 3.2 18.8 + - - +
114A TYR* 3.8 5.4 - - - +
115A ARG 3.3 1.4 - - - -
116A ILE* 1.3 84.8 - - + +
118A LYS* 1.3 60.6 + - - +
121A GLY* 4.5 2.7 - - - -
122A TYR 3.5 32.8 - - - +
123A LEU* 4.1 3.6 - - + +
168A PHE* 3.7 32.5 - - + -
206A LYS* 2.6 37.3 + - + -
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Residues in contact with LYS 118 (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 ARG* 6.0 1.8 - - - +
89A GLU* 3.4 32.5 - - + +
90A SER* 4.0 16.8 + - - +
91A PHE 2.9 19.9 + - - +
92A ASP* 3.5 30.1 + - - +
117A LEU* 1.3 77.7 - - - +
119A LYS* 1.3 65.8 + - - +
120A GLY 3.3 0.2 + - - -
121A GLY* 2.8 23.5 + - - +
206A LYS* 3.7 7.0 - - - +
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Residues in contact with LYS 119 (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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89A GLU* 4.3 17.7 + - - +
117A LEU 4.0 0.6 + - - -
118A LYS* 1.3 76.0 - - - +
120A GLY* 1.3 58.7 + - - +
121A GLY 3.6 0.2 + - - -
206A LYS* 4.0 12.8 - - - +
207A LYS 4.0 14.8 - - - +
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Residues in contact with GLY 120 (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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119A LYS* 1.3 72.5 - - - +
121A GLY* 1.3 62.9 - - - +
122A TYR* 3.7 21.1 + - - -
205A THR* 4.2 8.5 - - - +
206A LYS 2.6 18.9 + - - -
207A LYS* 3.9 5.0 + - - -
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Residues in contact with GLY 121 (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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92A ASP* 3.2 19.3 - - - -
117A LEU* 4.5 9.6 - - - -
118A LYS* 2.8 20.8 + - - +
119A LYS 3.2 0.8 + - - -
120A GLY* 1.3 82.6 - - - +
122A TYR* 1.3 59.5 + - - -
205A THR* 3.5 4.2 - - - -
206A LYS* 2.8 27.7 + - - -
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Residues in contact with TYR 122 (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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35A PRO* 3.6 30.5 - - + -
92A ASP 3.0 11.6 + - - -
93A PHE* 3.1 8.3 - - + +
94A ALA 2.9 25.5 + - - -
117A LEU* 3.5 8.7 - - - +
120A GLY 3.7 13.8 + - - -
121A GLY* 1.3 76.1 - - - -
123A LEU* 1.3 60.0 + - - +
124A ILE* 4.0 9.2 - - + -
203A ARG* 3.5 47.3 + - + -
204A GLY 3.3 7.9 - - - +
205A THR* 3.3 32.2 - - + +
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Residues in contact with LEU 123 (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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94A ALA* 3.5 28.0 - - + +
96A MSE 4.1 21.3 - - + -
110A LEU* 3.6 31.2 - - + -
113A ALA* 4.1 9.0 - - + -
117A LEU* 4.1 3.4 - - + +
122A TYR* 1.3 72.6 - - - +
124A ILE* 1.3 66.8 + - - +
125A VAL* 3.7 11.4 - - + -
163A MSE 3.7 17.1 - - + +
168A PHE* 3.6 34.7 - - + -
202A ILE 3.6 1.6 - - - +
203A ARG* 3.3 3.1 - - - -
204A GLY 2.9 31.6 + - - -
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Residues in contact with ILE 124 (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 VAL* 4.4 7.4 - - + +
33A LEU* 3.8 22.0 - - + +
34A LEU* 4.3 4.3 - - + -
35A PRO* 4.0 22.9 - - + -
93A PHE* 4.1 9.2 - - + -
94A ALA 2.8 17.3 + - - +
95A LEU* 3.3 22.8 - - + +
96A MSE 2.8 26.0 + - - -
122A TYR* 4.0 16.4 - - + +
123A LEU* 1.3 76.9 - - - +
125A VAL* 1.3 60.9 + - - +
201A VAL* 3.4 31.6 - - + -
202A ILE 3.3 4.3 - - - +
203A ARG* 3.9 10.3 - - + -
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Residues in contact with VAL 125 (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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96A MSE 3.3 20.6 - - + +
100A ILE* 4.2 14.6 - - + +
110A LEU* 4.7 4.7 - - + -
123A LEU* 3.7 29.6 - - + -
124A ILE* 1.3 77.4 - - - +
126A GLY* 1.3 62.2 + - - +
127A ILE* 4.2 10.9 + - + -
159A LEU* 3.7 27.3 - - + +
163A MSE 4.0 15.3 - - + -
200A VAL 3.7 1.6 - - - +
201A VAL* 3.4 4.7 - - - -
202A ILE* 2.8 38.8 + - - +
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Residues in contact with GLY 126 (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 VAL* 5.5 0.7 - - - -
95A LEU* 5.3 0.2 - - - +
96A MSE 2.8 13.2 + - - +
97A VAL* 4.5 6.1 - - - +
98A THR* 3.0 27.6 + - - +
124A ILE* 4.2 0.8 - - - +
125A VAL* 1.3 73.9 - - - +
127A ILE* 1.3 68.1 + - - +
199A PHE* 4.1 19.3 - - - -
200A VAL 3.3 7.6 - - - -
201A VAL* 4.3 6.9 - - - +
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Residues in contact with ILE 127 (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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98A THR* 4.5 4.0 - - - +
100A ILE* 4.1 22.0 - - + -
101A CYS* 4.3 13.5 - - - -
125A VAL* 4.2 1.1 - - + +
126A GLY* 1.3 80.8 - - - +
128A VAL* 1.3 62.5 + - - +
129A ASP* 3.6 8.7 + - - +
154A PHE* 3.7 28.7 - - + +
155A SER 4.1 15.3 - - - +
156A THR* 4.2 9.6 - - - +
159A LEU* 4.0 32.3 - - + -
199A PHE* 3.4 11.2 - - - -
200A VAL* 2.8 40.8 + - + +
202A ILE* 5.3 1.1 - - + -
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Residues in contact with VAL 128 (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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26A GLU* 5.1 5.4 - - - +
98A THR* 4.5 10.9 - - + +
101A CYS* 5.5 4.8 - - - -
127A ILE* 1.3 76.8 - - - +
129A ASP* 1.3 64.2 + - - +
130A ARG* 3.3 4.2 + - - -
132A SER* 4.2 0.4 - - - +
134A LEU* 4.3 12.1 - - + -
135A GLY* 3.8 31.2 - - - +
138A TYR* 4.2 29.6 - - + -
148A TYR* 5.9 0.7 - - - +
153A PHE* 5.4 8.5 - - + -
154A PHE 3.7 8.8 + - - +
177A LEU* 5.5 1.1 - - + -
198A ALA 3.2 11.9 - - - +
199A PHE* 4.3 13.7 - - + -
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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