Contacts of the strand formed by residues 199 - 205 (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 PHE 199 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU* 3.7 59.2 - - + -
29A ALA* 4.3 0.7 - - + -
30A VAL* 4.3 3.6 - - + -
97A VAL* 4.0 19.3 - - + -
98A THR* 4.2 13.0 - - + -
126A GLY* 4.1 13.2 - - - -
127A ILE 3.4 23.1 - - - -
128A VAL* 4.3 7.4 - - + +
175A GLN* 3.2 4.5 - - - +
176A THR* 2.9 46.9 + - + +
177A LEU* 4.0 13.2 - - + -
198A ALA* 1.3 77.5 - - - +
200A VAL* 1.3 61.3 + - - +
201A VAL* 3.4 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL 3.7 1.8 - - - +
126A GLY* 3.3 2.4 - - - -
127A ILE* 2.8 42.8 + - + +
129A ASP* 3.8 17.0 - - + +
156A THR* 3.5 30.5 - - + +
173A VAL* 3.3 31.0 - - + -
174A VAL 3.4 4.0 - - - +
175A GLN* 4.3 4.7 - - + -
194A TYR* 4.1 11.4 - - + -
197A GLY 3.9 13.9 - - - +
199A PHE* 1.3 79.1 - - - +
201A VAL* 1.3 67.2 + - - +
202A ILE* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 3.9 19.5 - - + +
30A VAL* 4.1 16.6 - - + -
33A LEU* 3.6 11.8 - - + +
124A ILE* 3.4 33.4 - - + -
125A VAL 3.4 7.6 - - - +
126A GLY* 4.3 1.8 - - - -
173A VAL* 3.3 5.7 - - - +
174A VAL* 2.9 42.4 + - + +
199A PHE* 3.4 31.2 - - + -
200A VAL* 1.3 78.5 - - - +
202A ILE* 1.3 60.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.2 2.2 - - - -
123A LEU 3.6 1.6 - - - +
124A ILE* 3.3 3.3 - - - -
125A VAL* 2.8 36.2 + - - +
127A ILE* 5.3 0.9 - - + -
156A THR* 3.8 32.5 - - + +
159A LEU* 3.5 31.0 - - + -
160A MSE 3.9 10.3 - - + -
163A MSE 3.9 14.1 - - - +
171A PHE* 3.8 26.5 - - + -
172A LYS 3.5 6.7 - - - +
173A VAL* 4.3 10.5 - - + -
200A VAL* 4.2 13.2 - - + -
201A VAL* 1.3 77.6 - - - +
203A ARG* 1.3 61.9 + - - +
204A GLY 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.6 40.7 + - + +
35A PRO* 5.4 5.4 - - - +
122A TYR* 3.5 60.0 + - + -
123A LEU 3.3 2.9 - - - +
124A ILE* 3.9 12.8 - - + +
170A GLU 4.0 7.1 + - - +
171A PHE* 3.2 11.0 - - - -
172A LYS* 2.8 68.4 + - + +
202A ILE* 1.3 74.7 - - - +
204A GLY* 1.3 60.2 + - - +
205A THR* 4.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.3 8.6 - - - +
123A LEU 2.9 34.3 + - - -
163A MSE 3.8 8.1 - - - +
168A PHE* 3.8 8.0 - - - -
169A GLU 3.6 7.4 - - - -
171A PHE* 3.7 17.3 - - - -
203A ARG* 1.3 74.9 - - - +
205A THR* 1.3 64.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY* 4.2 9.0 - - - +
121A GLY 3.5 9.6 - - - +
122A TYR* 3.3 27.2 - - + -
167A GLY 4.1 0.3 - - - +
168A PHE* 3.4 6.6 - - - -
169A GLU* 2.7 42.4 + - - +
170A GLU* 3.8 23.0 + - - +
203A ARG* 4.8 2.3 + - - -
204A GLY* 1.3 72.6 - - - -
206A LYS* 1.3 72.1 + - - +
207A LYS* 3.4 18.7 + - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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