Contacts of the strand formed by residues 955 - 962 (chain B) in PDB entry 2WIN
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 GLU 955 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 4.9 11.9 - - - +
176A LEU* 3.2 34.1 - - + +
177A VAL* 5.6 1.0 - - - +
954B SER* 1.3 74.7 - - - +
956B THR* 1.3 65.1 + - - +
957B ARG* 3.8 28.0 + - + -
1301B GLU* 4.8 10.7 - - + +
1302B THR 3.4 10.5 - - - +
1303B LYS* 4.1 13.8 - - + +
1323B VAL 4.5 0.2 - - - +
1324B THR* 3.7 3.3 - - - -
1325B MET* 3.2 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 956 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920B VAL* 4.8 1.1 - - + -
954B SER 5.1 0.5 + - - -
955B GLU* 1.3 73.7 - - - +
957B ARG* 1.3 64.0 + - - +
958B ILE* 4.1 4.7 + - + +
1300B GLU 3.6 1.4 - - - +
1301B GLU* 3.4 4.4 - - - -
1302B THR* 2.8 47.4 + - - +
1304B GLU 4.1 9.2 + - - -
1305B ASN* 4.2 15.0 + - - +
1306B GLU 5.2 2.0 + - - +
1308B PHE* 5.0 12.8 - - + -
1322B VAL* 3.8 22.0 - - + -
1324B THR* 3.2 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 957 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN* 5.8 5.4 - - - +
151A ILE* 5.2 11.2 - - - +
152A PRO 4.8 0.4 + - - -
153A VAL* 3.4 33.4 - - - +
174A PRO* 6.1 3.0 - - - +
177A VAL* 5.8 6.1 - - - +
955B GLU* 3.8 25.3 + - + +
956B THR* 1.3 74.4 - - - +
958B ILE* 1.3 71.6 + - - +
959B LEU* 4.0 6.3 + - + +
1299B SER* 4.2 9.9 + - - -
1300B GLU 3.4 6.7 - - - +
1301B GLU* 2.8 41.7 + - + +
1321B SER 4.1 0.7 - - - +
1322B VAL* 3.5 6.3 - - - +
1323B VAL* 3.1 39.9 + - + +
1325B MET* 6.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 958 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956B THR* 5.0 5.2 - - + +
957B ARG* 1.3 75.8 - - - +
959B LEU* 1.3 64.2 + - - +
960B LEU* 5.1 4.7 - - + +
1276B LEU* 4.1 30.3 - - + -
1278B LEU* 4.5 14.8 - - + -
1298B ARG 5.9 0.2 - - - +
1299B SER* 3.1 29.6 - - - -
1300B GLU* 2.8 27.8 + - + +
1302B THR* 6.0 1.8 - - + +
1308B PHE* 3.5 40.2 - - + -
1320B LEU* 3.8 23.6 - - + -
1322B VAL* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 959 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.1 37.2 - - + -
957B ARG* 5.3 6.3 - - + +
958B ILE* 1.3 75.6 - - - +
960B LEU* 1.3 75.6 + - - +
961B GLN* 3.8 22.7 - - + +
1297B LEU* 4.3 9.6 - - + -
1298B ARG 4.0 1.8 - - - +
1299B SER* 4.8 4.7 - - - +
1319B THR* 5.1 0.9 - - + +
1320B LEU* 3.2 12.1 - - - +
1321B SER* 3.0 54.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 960 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B LEU* 4.2 16.2 - - + -
958B ILE* 4.2 3.6 - - + -
959B LEU* 1.3 74.5 - - - +
961B GLN* 1.3 62.4 + - - +
1272B LEU* 6.5 0.2 - - + -
1274B VAL* 3.8 44.9 - - + -
1276B LEU* 4.9 16.6 - - + -
1287B HIS* 5.0 16.6 - - + +
1289B ILE* 4.9 16.6 - - + +
1296B LEU 4.0 2.3 - - - +
1297B LEU* 3.4 10.6 - - - +
1298B ARG* 3.0 42.5 + - + +
1300B GLU* 6.5 0.2 - - + -
1319B THR 3.9 4.0 - - - +
1320B LEU* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 961 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 5.6 0.2 - - - +
959B LEU* 3.8 15.1 - - + +
960B LEU* 1.3 76.7 - - - +
962B GLY* 1.3 72.8 + - - +
963B THR* 5.0 3.8 - - - +
1289B ILE* 5.9 1.3 - - - -
1295B SER* 4.7 5.6 + - - +
1296B LEU 5.3 0.2 - - - -
1297B LEU* 3.3 37.3 - - + +
1318B GLY* 3.5 1.6 - - - -
1319B THR* 2.8 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 962 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961B GLN* 1.3 85.5 + - - +
963B THR* 1.3 59.4 + - - -
964B PRO* 2.9 20.3 - - - +
1270B LEU* 5.1 5.6 - - - -
1272B LEU* 5.8 2.7 - - - -
1289B ILE* 4.8 12.7 - - - +
1294B ALA 4.4 17.6 + - - -
1295B SER* 4.5 9.3 - - - +
1317B GLN 4.5 1.1 - - - -
1318B GLY* 4.4 5.2 - - - -
----------------------------------------------------------
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