Contacts of the strand formed by residues 122 - 128 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 3.1 37.4 + - - +
119B PHE 4.3 2.9 - - - -
120B GLY 3.2 14.5 + - - -
121B SER* 1.3 75.0 - - - +
123B TRP* 1.3 68.8 + - - +
139B THR 3.2 15.3 - - - -
140B SER* 4.1 2.9 - - - -
141B ASN 3.9 4.3 - - - +
159B LEU* 3.0 32.1 + - - +
160B TRP* 3.4 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLN* 3.1 16.0 + - - -
73B ASN* 3.4 46.5 - - + +
74B HIS* 3.7 18.8 - + - -
77B TYR* 3.9 10.5 - - + -
118B ASN* 3.0 9.5 + - - -
122B SER* 1.3 78.3 - - - +
124B THR* 1.3 58.4 + - - +
125B TRP* 3.2 30.6 - + + +
138B ASN* 3.5 0.2 - - - -
139B THR* 2.8 40.4 + - - +
141B ASN 3.0 28.3 + - - -
143B ALA 4.2 6.3 - - - -
156B THR* 3.5 19.1 - - + +
157B VAL 3.5 5.2 - - - -
158B ASP* 3.4 50.0 - - + -
159B LEU* 4.2 0.4 - - - -
160B TRP* 3.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.4 42.0 - - + +
114B SER* 4.1 1.8 - - - -
115B ALA* 3.4 15.1 - - - -
118B ASN* 3.3 10.4 + - - -
123B TRP* 1.3 70.5 - - - +
125B TRP* 1.3 64.8 + - - +
136B ILE* 4.1 9.9 - - + -
137B VAL 3.8 1.6 - - - -
138B ASN* 2.6 23.6 + - - +
156B THR* 3.2 3.5 + - - -
157B VAL* 3.0 47.7 + - - -
159B LEU* 3.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TRP* 4.0 7.2 - + - -
73B ASN* 3.3 32.1 - - + -
76B PHE* 4.0 15.7 - + - -
111B PHE* 3.6 6.3 - - - -
123B TRP* 3.2 27.4 - + + +
124B THR* 1.3 76.5 - - - +
126B LEU* 1.3 58.7 + - - +
127B VAL* 3.9 17.0 - - + -
135B ALA 3.8 0.2 - - - +
136B ILE* 3.2 9.7 - - - +
137B VAL* 2.8 48.5 + - + +
139B THR* 3.0 25.1 + - + -
143B ALA 4.2 0.9 - - - -
144B THR* 3.7 11.0 - - - -
145B PRO* 3.3 31.4 - - + +
153B PRO* 3.9 19.7 - - + -
155B LEU 3.3 7.2 - - - +
156B THR* 3.3 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 5.9 0.2 - - + -
97B ILE* 4.3 20.6 - - + -
101B PHE* 3.9 18.8 - - + -
107B PHE* 3.9 38.4 - - + -
111B PHE* 3.6 3.1 - - + -
125B TRP* 1.3 73.0 - - - +
127B VAL* 1.3 59.5 + - - +
134B LEU* 4.2 6.7 - - + -
135B ALA 3.4 18.8 - - - +
136B ILE* 4.7 0.4 - - - +
153B PRO* 4.0 0.3 - - - +
154B LEU* 2.8 54.4 + - + +
155B LEU* 2.9 28.1 + - + +
188B VAL* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TRP* 3.9 10.8 - - + -
126B LEU* 1.3 77.8 - - - +
128B LYS* 1.3 60.1 + - - +
129B ASN* 4.3 9.2 - - - +
134B LEU* 3.3 7.8 - - - +
135B ALA* 2.9 47.3 + - + +
137B VAL* 3.9 21.1 - - + -
145B PRO* 3.7 35.7 - - + -
151B VAL* 3.6 20.6 - - + -
152B THR 3.4 6.3 - - - +
153B PRO* 4.2 4.7 - - + -
154B LEU* 3.9 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 1.3 71.2 - - - +
129B ASN* 1.3 74.2 + - - +
132B GLY* 3.9 22.7 - - - +
133B SER 3.4 4.0 - - - -
134B LEU* 4.3 4.9 - - + -
150B GLY 3.9 1.5 - - - +
151B VAL* 3.4 2.9 - - - +
152B THR* 2.9 55.5 + - - +
154B LEU* 3.8 14.5 - - + +
191B ASN 3.4 3.8 + - - -
192B LEU* 2.7 43.5 + - + +
193B ALA 4.3 0.6 - - - -
194B LYS 3.3 21.5 - - - -
----------------------------------------------------------
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