Contacts of the strand formed by residues 163 - 172 (chain A) in PDB entry 5F02
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 163 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.8 2.7 - - - -
25A CYS* 3.4 34.2 - - + +
134A VAL 3.8 0.2 - - - +
135A ALA* 3.4 1.4 - - - -
136A ILE* 2.8 38.4 + - + +
138A ALA* 3.5 32.8 - - + -
143A PHE* 4.2 9.0 - + - -
162A ASP* 1.3 81.8 + - - +
164A GLY* 1.3 60.7 + - - +
165A VAL* 3.3 22.0 - - + +
187A ASN* 2.8 24.6 + - - -
188A SER* 4.5 0.7 - - - -
189A TRP* 3.6 30.1 - + - -
302A 5T9 3.1 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A CYS* 3.5 37.3 - - - +
28A PHE* 5.8 0.2 - - - +
29A SER* 3.8 7.0 + - - -
70A MET* 4.0 15.3 - - - -
134A VAL 3.4 7.9 - - - -
163A HIS* 1.3 74.1 - - - +
165A VAL* 1.3 66.0 + - - +
188A SER* 4.8 2.8 + - - -
302A 5T9 3.6 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 2.7 27.2 + - - +
134A VAL* 2.8 43.3 + - + +
136A ILE* 4.1 22.4 - - + -
143A PHE* 5.3 0.4 - - + -
163A HIS* 3.3 31.2 - - + +
164A GLY* 1.3 77.7 - - - +
166A LEU* 1.3 60.1 + - - +
185A VAL* 3.5 22.7 - - + -
186A LYS 3.6 12.1 - - - +
187A ASN* 3.6 15.0 - - - +
188A SER* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 5.0 4.0 - - + -
28A PHE 5.6 0.4 - - - +
29A SER* 3.8 12.8 - - - +
32A GLY* 3.7 23.6 - - - +
33A ALA* 3.4 27.8 - - - +
131A PRO* 3.8 17.9 - - + -
132A ILE 3.5 23.1 - - - +
133A SER 3.9 0.7 - - - +
165A VAL* 1.3 79.3 - - - +
167A VAL* 1.3 62.2 + - - +
168A VAL* 3.5 21.1 + - + -
185A VAL* 3.3 3.7 - - - -
186A LYS* 2.8 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 4.7 4.7 - - + -
126A VAL* 3.7 26.4 - - + +
130A GLY 4.5 0.5 - - - +
131A PRO* 3.2 5.2 - - - +
132A ILE* 2.8 39.3 + - + +
134A VAL* 3.8 33.9 - - + -
165A VAL 4.3 0.6 - - - -
166A LEU* 1.3 69.5 - - - +
168A VAL* 1.3 60.4 + - - +
169A GLY 3.3 26.2 - - - +
183A TRP* 3.8 11.4 - - + -
184A LEU 3.5 4.9 - - - +
185A VAL* 3.9 7.0 - - + +
211A ILE* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASP* 3.7 0.6 - - - +
7A TRP* 2.8 39.4 + - - -
8A ARG* 4.3 8.3 - - + -
13A VAL* 4.0 27.8 - - + -
126A VAL* 4.5 0.2 - - - -
131A PRO* 4.3 7.2 - - + -
166A LEU* 3.8 31.6 - - + +
167A VAL* 1.3 76.1 - - - +
169A GLY* 1.3 57.2 + - - +
184A LEU* 2.9 42.0 + - + +
186A LYS* 4.1 9.6 - - + -
198A TYR* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL 3.1 15.3 - - - -
6A ASP* 4.4 0.2 - - - -
126A VAL* 3.8 12.5 - - - +
167A VAL* 3.3 16.0 - - - +
168A VAL* 1.3 80.6 - - - +
170A TYR* 1.3 65.8 - - - +
183A TRP* 3.7 0.7 - - - -
184A LEU* 2.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 3.4 18.7 - - - +
2A PRO* 2.7 31.6 + - - +
3A ARG 3.6 15.9 - - - -
4A SER* 3.3 4.3 - - - -
5A VAL* 2.9 56.3 + - + +
123A MET* 3.6 34.1 - - + -
126A VAL* 3.9 13.5 - - + -
127A ALA* 3.8 1.8 - - - +
169A GLY* 1.3 78.1 - - - +
171A GLY* 1.3 61.0 - - - +
182A TYR* 3.2 20.6 - - - +
183A TRP* 3.8 22.2 - + + -
184A LEU* 4.1 4.8 - - - +
203A LYS* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG 4.0 7.2 - - - -
4A SER* 4.0 15.7 - - - -
170A TYR* 1.3 78.9 - - - +
172A PHE* 1.3 64.0 + - - +
181A LYS* 3.4 8.1 - - - +
182A TYR* 3.0 41.4 + - - +
203A LYS* 5.1 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 3.5 69.3 - - + +
4A SER* 4.8 7.1 - - - -
171A GLY* 1.3 79.3 - - - +
173A GLU* 1.3 68.0 + - - +
174A SER* 3.6 21.8 + - - -
180A ASN* 3.1 26.2 - - - +
181A LYS* 4.4 7.4 - - + -
182A TYR* 3.6 16.3 + - - -
----------------------------------------------------------
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