Contacts of the strand formed by residues 124 - 132 (chain A) in PDB entry 2W5X
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 LYS 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 5.4 9.9 + - - -
123A ILE* 1.3 75.2 - - - +
125A THR* 1.3 59.8 + - - +
164A ASP* 3.3 24.4 + - + +
209A ARG* 3.8 29.6 - - - +
241A PHE* 6.1 1.8 - - + -
242A LEU* 3.7 35.0 - - + +
244A LYS 6.1 0.2 - - - -
245A ASP* 5.9 2.7 - - - -
247A SER* 3.1 23.2 + - - +
248A ALA 3.0 10.7 + - - +
249A PHE* 3.1 3.9 - - - +
250A PHE 2.8 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.9 27.6 - - + +
118A ALA* 3.7 23.1 - - + -
119A ALA* 4.7 2.2 - - + +
123A ILE 3.7 10.8 - - - +
124A LYS* 1.3 81.4 - - - +
126A GLY* 1.3 58.5 + - - +
162A ASP* 3.6 6.2 + - - +
163A LEU* 3.5 29.4 - - - +
164A ASP* 3.0 31.5 + - - +
165A PHE 3.1 6.1 + - - -
242A LEU* 3.4 7.0 - - - +
250A PHE* 3.3 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 5.8 0.4 - - - +
125A THR* 1.3 76.3 - - - +
127A VAL* 1.3 66.8 + - - +
128A VAL* 5.5 0.4 - - - -
163A LEU* 3.8 0.7 - - - -
165A PHE* 3.1 17.9 - - - -
238A ALA* 5.5 0.4 - - - -
242A LEU* 3.5 12.9 - - - +
250A PHE* 3.0 11.3 + - - +
251A ILE* 3.4 8.4 - - - -
252A MET 3.0 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.9 4.5 - - + -
126A GLY* 1.3 78.9 - - - +
128A VAL* 1.3 66.3 + - - +
133A ILE* 3.8 11.2 - - + +
138A PRO* 3.4 38.1 - - + +
141A PHE* 4.1 24.7 - - + +
142A TYR* 4.8 3.8 - - + -
163A LEU* 4.0 27.4 - - + -
165A PHE* 3.0 7.5 + - - -
166A PHE* 3.0 26.2 - - - +
167A ALA 3.1 3.3 + - - -
250A PHE* 5.9 0.2 - - + -
252A MET* 3.4 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 1.3 82.1 - - - +
129A ALA* 1.3 66.6 + - - +
165A PHE* 4.1 22.9 - - + -
167A ALA* 3.3 12.1 - - + +
230A PHE* 4.2 6.1 - - + -
231A LEU* 3.8 21.8 - - + -
234A ALA* 3.8 32.3 - - + +
235A THR* 4.6 1.1 - - - +
238A ALA* 4.6 7.4 - - + -
251A ILE* 5.1 1.8 - - + -
252A MET* 2.8 9.8 + - - +
253A SER* 3.3 21.1 - - - +
254A GLU* 2.8 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 1.3 78.4 - - - +
130A THR* 1.3 62.6 + - - +
131A SER* 3.3 10.0 - - - +
133A ILE* 4.4 5.3 - - + +
138A PRO* 3.8 30.1 - - + -
167A ALA 3.0 7.7 + - - -
168A GLY* 3.2 24.1 - - - -
220A MET* 4.2 0.3 - - - +
230A PHE* 3.5 9.0 - - - -
254A GLU* 3.7 13.0 - - + +
256A SER* 3.5 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 1.3 72.3 - - - +
131A SER* 1.3 60.8 + - - +
220A MET* 3.1 23.9 + - - +
227A ARG* 3.6 41.6 + - - +
230A PHE* 4.2 11.9 - - + -
231A LEU* 4.2 14.8 - - + -
254A GLU 3.5 10.5 + - - +
255A GLY* 4.2 1.1 - - - -
256A SER* 3.0 28.2 + - - +
257A GLN* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 3.5 11.3 - - - +
130A THR* 1.3 79.5 - - - +
132A SER* 1.3 76.6 + - - +
133A ILE 3.4 0.2 + - - -
135A GLU* 3.4 18.7 + - - +
138A PRO* 4.5 0.3 - - - +
168A GLY* 4.0 0.5 - - - -
169A GLY 3.1 18.4 + - - -
219A ALA* 4.2 4.7 - - - -
254A GLU* 4.0 3.3 + - - -
256A SER* 3.2 23.6 + - - -
260A TRP* 3.7 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 1.3 89.8 + - - +
133A ILE* 1.3 64.2 + - - +
134A THR* 2.6 31.2 + - - -
135A GLU* 3.1 15.7 + - - +
138A PRO* 3.9 2.9 - - - +
151A GLU* 4.5 3.1 - - - -
169A GLY* 3.5 11.0 - - - -
170A GLY* 3.4 21.0 - - - +
173A TYR* 3.8 10.1 - - - -
218A GLU* 4.0 7.6 - - - -
219A ALA* 4.0 8.2 - - - +
----------------------------------------------------------
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