Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 2W7W
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 SER 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASN* 3.1 37.1 + - - +
119A PHE 4.5 2.7 - - - -
120A GLY 3.2 13.7 + - - -
121A SER* 1.3 76.5 - - - +
123A TRP* 1.3 70.4 + - - +
139A THR 3.2 15.9 - - - -
140A SER* 4.4 1.6 - - - -
141A ASN 4.0 3.8 - - - +
159A LEU* 2.8 33.1 + - - +
160A TRP* 3.4 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLN* 3.0 22.0 + - - -
73A ASN* 3.5 41.6 - - + +
74A HIS* 3.6 21.3 - + - -
77A TYR* 4.0 9.6 - - + -
118A ASN* 3.0 7.5 + - - -
122A SER* 1.3 80.6 - - - +
124A THR* 1.3 59.7 + - - +
125A TRP* 3.4 17.4 - + + +
138A ASN* 3.4 0.3 - - - -
139A THR* 2.8 48.5 + - - +
141A ASN 2.8 30.6 + - - -
143A ALA 4.1 6.1 - - - -
156A THR* 3.7 16.8 - - + +
157A VAL 3.4 5.6 - - - -
158A ASP* 3.4 52.5 - - + -
159A LEU* 4.2 0.7 - - - -
160A TRP* 3.5 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 3.5 34.6 - - + +
114A SER* 3.8 9.6 - - - +
115A ALA* 3.3 16.6 - - - -
118A ASN* 3.2 10.6 + - - -
123A TRP* 1.3 71.9 - - - +
125A TRP* 1.3 63.5 + - - +
136A ILE* 3.9 9.9 - - + -
137A VAL 3.7 3.4 - - - -
138A ASN* 2.8 23.4 + - - +
156A THR* 3.1 4.2 + - - -
157A VAL* 2.9 39.8 + - - -
159A LEU* 3.3 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TRP* 4.1 6.3 - + - -
73A ASN* 3.3 35.4 - - + -
76A PHE* 3.9 16.8 - + - -
111A PHE* 3.8 5.8 - - - -
123A TRP* 3.4 22.3 - + + +
124A THR* 1.3 73.1 - - - +
126A LEU* 1.3 58.7 + - - +
127A VAL* 3.7 17.5 - - + -
135A ALA 3.7 0.2 - - - +
136A ILE* 3.2 9.5 - - - +
137A VAL* 2.7 52.9 + - + +
139A THR* 2.9 23.8 + - + -
144A THR* 3.7 10.3 - - - -
145A PRO* 3.2 32.8 - - + +
153A PRO* 4.0 17.5 - - + -
155A LEU 3.3 9.4 - - - +
156A THR* 3.3 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 5.7 0.7 - - + -
97A ILE* 4.4 18.2 - - + -
101A PHE* 4.0 16.6 - - + -
107A PHE* 4.1 22.4 - - + -
111A PHE* 3.7 11.0 - - + -
125A TRP* 1.3 71.9 - - - +
127A VAL* 1.3 61.5 + - - +
134A LEU* 3.8 28.0 - - + -
135A ALA 3.4 16.2 - - - +
136A ILE* 4.6 0.9 - - + +
153A PRO* 4.2 0.2 - - - +
154A LEU* 2.9 46.2 + - + +
155A LEU* 2.9 26.5 + - + +
185A TRP* 5.4 0.2 - - + -
188A VAL* 4.6 10.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
125A TRP* 3.7 21.1 - - + -
126A LEU* 1.3 80.6 - - - +
128A LYS* 1.3 60.2 + - - +
129A ASN* 4.0 9.4 - - - +
134A LEU* 3.4 6.1 - - - +
135A ALA* 2.9 54.0 + - + +
137A VAL* 3.9 21.5 - - + -
145A PRO* 3.9 18.6 - - + -
151A VAL* 3.6 22.9 - - + -
152A THR 3.4 6.3 - - - +
153A PRO* 4.4 4.0 - - + -
154A LEU* 4.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 1.3 72.8 - - - +
129A ASN* 1.3 80.6 + - - +
130A ALA 4.9 3.6 + - - -
132A GLY* 3.9 25.9 - - - +
133A SER 3.8 2.2 - - - -
134A LEU* 4.2 4.9 - - + -
150A GLY 3.9 2.6 + - - +
151A VAL* 3.4 1.7 - - - -
152A THR* 2.7 55.5 + - - +
154A LEU* 3.9 14.5 - - + +
191A ASN 5.1 1.1 - - - -
192A LEU* 3.7 35.7 - - + +
194A LYS 3.7 23.8 + - - -
----------------------------------------------------------
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