Contacts of the strand formed by residues 199 - 205 (chain B) 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 PHE 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B GLU* 3.6 60.1 - - + -
29B ALA* 4.4 0.4 - - + +
30B VAL* 4.3 3.6 - - + -
97B VAL* 3.9 20.9 - - + -
98B THR* 4.2 7.9 - - - -
126B GLY* 3.8 17.7 - - - -
127B ILE 3.4 24.5 - - - -
128B VAL* 4.1 7.4 - - + +
175B GLN* 3.3 3.5 - - - +
176B THR* 2.8 49.8 + - + +
177B LEU* 4.2 9.9 - - + -
198B ALA* 1.3 77.3 - - - +
200B VAL* 1.3 60.9 + - - +
201B VAL* 3.5 28.4 + - + +
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Residues in contact with VAL 200 (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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125B VAL 3.7 1.4 - - - +
126B GLY* 3.2 2.9 - - - -
127B ILE* 2.9 42.8 + - + +
129B ASP* 4.1 12.1 - - + +
156B THR* 3.5 31.6 - - + +
173B VAL* 3.6 26.9 - - + -
174B VAL 3.5 4.0 - - - +
175B GLN* 4.3 6.5 - - + -
194B TYR* 4.2 11.7 - - + -
195B GLY 5.2 0.4 - - - +
197B GLY 3.9 16.2 - - - +
199B PHE* 1.3 79.8 - - - +
201B VAL* 1.3 65.5 + - - +
202B ILE* 4.1 7.0 - - + -
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Residues in contact with VAL 201 (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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29B ALA* 3.7 26.9 - - + -
30B VAL* 3.9 14.6 - - + +
33B LEU* 3.6 12.9 - - + +
124B ILE* 3.2 34.3 - - + -
125B VAL 3.3 6.5 - - - +
126B GLY* 4.5 0.9 - - - -
173B VAL* 3.3 6.1 - - - +
174B VAL* 3.0 40.8 + - + +
199B PHE* 3.5 31.0 - - + -
200B VAL* 1.3 73.4 - - - +
202B ILE* 1.3 60.4 + - - +
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Residues in contact with ILE 202 (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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33B LEU* 4.4 2.2 - - - -
123B LEU 3.7 1.4 - - - +
124B ILE* 3.4 2.2 - - - +
125B VAL* 2.8 38.0 + - - +
127B ILE* 5.3 1.1 - - + -
156B THR* 3.7 32.8 - - + +
159B LEU* 3.5 28.9 - - + -
160B MSE 3.8 17.3 - - + +
163B MSE 4.1 12.1 - - - +
171B PHE* 3.7 26.5 - - + -
172B LYS 3.4 8.1 - - - +
173B VAL* 4.1 8.1 - - + +
200B VAL* 4.1 12.6 - - + +
201B VAL* 1.3 78.5 - - - +
203B ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 203 (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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33B LEU* 3.3 40.8 + - + +
35B PRO* 4.9 1.0 - - - +
122B TYR* 3.0 64.3 + - + -
123B LEU 3.3 7.0 - - - +
124B ILE* 3.8 9.9 - - + -
170B GLU 3.9 10.8 + - - +
171B PHE* 3.2 11.0 - - - -
172B LYS* 2.8 67.1 + - + +
202B ILE* 1.3 74.3 - - - +
204B GLY* 1.3 61.0 + - - +
205B THR* 3.4 9.3 + - - -
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Residues in contact with GLY 204 (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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122B TYR* 3.2 7.5 - - - +
123B LEU 2.8 33.8 + - - -
163B MSE 3.6 7.5 - - - +
168B PHE* 3.9 8.8 - - - -
169B GLU 3.6 8.5 - - - -
171B PHE* 3.8 17.5 - - - -
203B ARG* 1.3 74.5 - - - +
205B THR* 1.3 63.7 + - - -
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Residues in contact with THR 205 (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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120B GLY* 4.1 9.2 - - - +
121B GLY 3.4 11.2 - - - +
122B TYR* 3.1 31.0 - - + +
167B GLY 4.1 0.3 - - - +
168B PHE* 3.4 6.0 - - - -
169B GLU* 2.8 37.9 + - - +
170B GLU* 3.7 19.2 + - + +
203B ARG* 3.4 7.1 + - - -
204B GLY* 1.3 72.0 - - - -
206B LYS* 1.3 72.5 + - - +
207B LYS* 3.5 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