Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 1W7L
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 THR 175 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 3.7 12.5 + - - +
119A ILE* 3.7 26.8 - - + +
170A LYS 3.9 4.3 + - - -
171A PHE* 3.5 8.3 - - + -
172A THR* 2.9 36.6 + - - +
173A SER 3.4 3.0 - - - +
174A ARG* 1.3 76.0 - - - +
176A LYS* 1.3 61.6 + - - +
177A ALA 3.9 14.1 - - - +
206A HIS 5.2 1.0 - - - +
207A ASP 4.7 3.8 - - - +
208A VAL* 3.6 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.5 39.9 + - + +
112A VAL* 4.9 5.2 - - + -
116A ASP* 3.2 41.1 - - + +
117A GLU 2.9 9.4 + - - +
174A ARG 3.1 2.0 + - - +
175A THR* 1.3 73.7 - - - +
177A ALA* 1.3 64.0 + - + +
207A ASP 5.0 0.6 - - - +
208A VAL* 3.7 4.9 - - - +
209A VAL* 3.1 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 5.7 2.9 - - + -
112A VAL* 5.1 4.0 - - + -
117A GLU 3.6 2.7 + - - +
118A VAL* 3.3 20.9 - - + -
119A ILE 2.9 21.7 + - - -
175A THR* 3.8 5.6 - - - +
176A LYS* 1.3 83.1 - - + +
178A LEU* 1.3 60.7 - - - +
208A VAL* 3.6 5.6 - - - -
209A VAL* 3.1 16.2 - - + +
211A ILE* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.5 30.7 - - + +
121A ILE* 4.2 13.2 - - + -
167A LEU* 4.0 12.8 - - + -
171A PHE* 3.8 26.2 - - + -
177A ALA* 1.3 75.4 - - - +
179A VAL* 1.3 79.4 + - - +
180A LEU* 3.8 13.9 - - + +
199A VAL* 4.0 25.6 - - + -
203A CYS* 4.4 14.1 - - - -
208A VAL* 3.7 3.1 - - + +
209A VAL 3.0 6.2 + - - +
210A CYS* 3.5 4.8 - - - -
211A ILE 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 5.0 1.8 - - + -
108A PHE* 3.8 21.3 - - + -
118A VAL* 3.7 25.8 - - + -
119A ILE 2.9 16.6 + - - +
120A ILE* 4.5 7.6 - - + -
121A ILE* 3.9 17.5 + - - +
128A TYR* 3.5 46.9 - - + +
178A LEU* 1.3 78.9 - - - +
180A LEU* 1.3 61.5 - - - +
181A ASN 4.0 1.0 + - - -
211A ILE* 3.4 24.0 - - + +
213A ASP* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 4.4 6.3 - - + -
178A LEU* 3.8 7.7 + - + -
179A VAL* 1.3 74.3 - - - +
181A ASN* 1.3 57.7 + - - +
182A THR* 4.3 8.7 - - + -
191A PHE* 3.7 44.6 - - + -
196A LEU* 3.6 26.5 - - + -
199A VAL* 4.9 6.7 - - + -
210A CYS* 3.9 14.6 - - - -
211A ILE 2.8 9.3 + - - +
212A THR* 3.3 18.1 + - - +
213A ASP* 2.7 32.4 + - - +
229A ILE* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 5.5 1.6 - - - +
124A PHE* 6.3 0.7 - - - -
125A PHE* 4.5 2.1 + - - +
128A TYR* 3.2 30.4 + - + +
179A VAL 4.0 2.0 + - - -
180A LEU* 1.3 74.9 - - - +
182A THR* 1.3 62.0 + - - +
183A PRO 3.4 12.1 + - - -
184A ASN* 3.5 24.6 + - - +
185A ASN 3.0 31.2 + - - +
191A PHE* 3.9 8.7 - - - -
213A ASP* 2.8 39.6 + - - -
215A VAL* 5.0 1.6 - - - +
1247A PLP 3.5 14.8 - - - +
----------------------------------------------------------
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