Contacts of the strand formed by residues 149 - 156 (chain B) in PDB entry 4YCV
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 149 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA 4.1 7.6 - - - +
147B GLN* 3.2 21.4 + - + +
148B LYS* 1.3 82.5 - - - +
150B ARG* 1.3 69.9 + - - +
151B PHE* 3.9 30.1 - - + -
164B LEU* 3.6 26.7 - - + -
165B ALA 3.5 16.4 - - - +
166B ASN* 4.1 15.3 - - + +
177B PHE* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 6.5 0.2 - - - -
143B SER 4.6 8.2 + - - +
144B ALA* 3.5 26.3 + - - +
147B GLN 4.3 16.8 + - - +
149B LEU* 1.3 82.2 - - - +
151B PHE* 1.3 68.3 + - - +
152B PHE* 4.1 20.0 - - + -
163B VAL 3.5 1.3 - - - +
164B LEU* 3.5 4.7 - - - +
165B ALA* 2.9 40.2 + - + +
177B PHE* 4.0 14.3 - - + -
178B ALA* 3.9 13.7 + - - +
181B TYR* 3.3 37.7 + - - +
182B ASP* 2.7 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 5.6 0.4 - - - +
143B SER* 3.2 47.1 + - - +
149B LEU* 3.9 35.4 - - + -
150B ARG* 1.3 78.0 - - - +
152B PHE* 1.3 70.8 + - - +
162B GLN* 3.0 27.4 - - - +
163B VAL 3.3 4.3 - - - -
164B LEU* 3.5 32.5 - - + -
199B SER* 5.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ILE* 3.8 24.5 - - + -
141B ARG* 3.3 9.6 - - - +
142B VAL* 3.6 42.2 - - + -
143B SER 5.5 0.4 - - - -
150B ARG* 4.1 26.7 - - + -
151B PHE* 1.3 76.5 - - - +
153B ASP* 1.3 66.0 + - - +
162B GLN* 3.1 10.0 - - - +
163B VAL* 2.9 54.6 + - + -
165B ALA* 4.7 1.3 - - + -
181B TYR* 4.0 39.7 - + - -
184B ILE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ARG 3.6 0.2 - - - +
139B ILE* 3.6 2.6 - - - -
140B MET* 2.9 34.8 + - + +
141B ARG* 3.1 46.1 + - + +
152B PHE* 1.3 81.7 - - - +
154B LEU* 1.3 62.6 + - - +
155B VAL* 3.7 2.1 + - + -
160B LYS* 3.9 33.8 - - + +
161B ILE 3.7 2.2 - - - -
162B GLN* 4.0 11.3 - - - +
203B GLU* 5.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 3.8 4.9 - - + +
135B ILE* 4.5 8.1 - - + -
136B THR 4.2 7.4 - - - +
137B GLY* 3.5 43.1 - - - +
138B ARG 3.7 1.6 - - - +
139B ILE* 3.7 24.0 - - + -
152B PHE 3.9 2.0 - - - -
153B ASP* 1.3 71.2 - - - +
155B VAL* 1.3 61.3 + - - +
160B LYS* 3.4 1.4 - - - -
161B ILE* 2.8 64.4 + - + +
163B VAL* 3.5 14.3 - - + +
190B VAL* 3.8 9.9 - - + -
192B ILE* 3.9 21.5 - - + -
206B ILE* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 3.5 3.4 - - - -
137B GLY* 3.6 3.8 - - - -
138B ARG* 2.9 44.5 + - + +
140B MET* 3.4 41.5 - - + -
153B ASP* 4.2 4.7 - - + +
154B LEU* 1.3 79.5 - - - +
156B GLY* 1.3 60.8 + - - +
158B GLY 5.9 0.9 - - - -
159B GLU 3.2 9.9 - - - +
160B LYS* 4.1 18.4 - - + -
242B LEU* 5.5 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASP* 5.2 5.6 - - - -
112B ILE* 3.4 15.3 - - - +
113B PRO* 4.0 7.6 - - - +
136B THR 5.6 0.2 - - - -
137B GLY* 5.4 2.0 - - - -
155B VAL* 1.3 77.7 - - - +
157B ASP* 1.3 74.0 + - - +
158B GLY 2.9 4.9 + - - +
159B GLU* 2.9 18.0 + - - +
----------------------------------------------------------
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