Contacts of the strand formed by residues 97 - 103 (chain B) in PDB entry 2W3S
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 PRO 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.5 43.5 - - + -
38B GLY 3.3 7.9 - - - +
39B LEU* 3.6 11.4 - - + -
84B PRO 6.1 0.4 - - - +
85B VAL 3.6 17.9 - - - +
86B LEU* 3.8 1.3 - - + -
87B ALA* 3.1 24.0 + - - +
93B PHE* 4.8 1.8 - - + -
95B GLY 3.4 6.7 - - - +
96B GLN* 1.3 93.8 + - + +
98B ILE* 1.3 60.1 + - - +
237B HIS* 5.1 8.7 - - + -
265B ILE* 4.3 14.8 - - + -
299B TRP* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 2.7 12.1 + - - +
39B LEU 4.3 1.3 - - - -
40B SER* 3.5 32.5 - - - +
47B ILE* 4.0 20.6 - - + -
50B LEU* 4.2 31.3 - - + +
65B PHE 4.3 0.5 - - - +
66B THR* 4.4 6.2 + - - -
67B ALA 4.5 1.2 + - - -
86B LEU* 3.7 21.0 - - - +
87B ALA* 3.8 21.2 + - + +
91B VAL* 3.7 13.0 - - + -
96B GLN 3.3 11.9 - - - +
97B PRO* 1.3 73.9 - - - +
99B PHE* 1.3 65.1 + - + +
118B ILE* 4.4 9.0 - - + -
120B TYR* 4.0 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.4 7.8 - - - -
38B GLY* 2.7 47.7 + - - +
50B LEU* 4.6 2.5 - - + -
52B LEU* 3.6 28.0 - - + -
55B VAL* 3.7 14.6 - - + -
64B VAL* 4.2 8.3 - - + -
65B PHE 3.1 15.5 - - - +
66B THR* 4.4 2.2 - - - +
86B LEU* 3.9 4.9 - - - -
98B ILE* 1.3 88.3 - - + +
100B LEU* 1.3 61.1 + - - +
101B VAL* 3.7 26.5 - - + -
113B ALA 3.2 25.6 - - - -
116B ALA* 3.5 27.6 - - + -
118B ILE* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.8 22.4 - - + -
36B ALA 3.7 3.6 - - - +
37B PHE* 4.0 9.9 - - + -
64B VAL* 3.2 5.4 - - - +
65B PHE* 2.6 67.7 + - + +
70B LEU* 6.4 1.3 - - + -
86B LEU* 4.4 8.3 - - + -
99B PHE* 1.3 75.2 - - - +
101B VAL* 1.3 67.7 + - - +
241B ALA* 3.7 34.1 - - + +
244B VAL* 5.7 3.4 - - + -
245B ALA* 4.2 4.9 - - + +
255B MET* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS 3.4 1.2 - - - +
35B LEU* 3.1 10.1 - - - +
36B ALA 2.8 36.7 + - - +
55B VAL* 3.9 11.7 - - + -
61B VAL* 3.8 37.2 - - + -
63B ALA 3.5 2.7 - - - +
64B VAL* 4.6 1.3 - - + +
99B PHE* 3.7 25.1 - - + -
100B LEU* 1.3 79.6 - - - +
102B ALA* 1.3 64.4 + - - +
109B ALA* 4.2 12.7 - - + +
112B ALA* 4.3 7.4 - - + -
113B ALA* 3.9 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.1 19.7 - - + -
34B HIS 3.3 4.7 - - - -
35B LEU* 3.7 17.5 - - + -
61B VAL* 3.5 1.7 - - - +
62B ILE* 2.6 30.6 + - - -
63B ALA* 2.7 35.1 + - + +
65B PHE* 4.3 9.8 - - + -
100B LEU 4.2 0.4 + - - -
101B VAL* 1.3 71.3 - - - +
103B ALA* 1.3 56.4 + - - +
245B ALA* 4.8 1.1 - - + -
249B THR* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.7 5.7 - - - +
34B HIS* 2.8 31.6 + - - +
60B GLY 3.2 16.6 - - - +
61B VAL* 3.5 20.0 - - + -
62B ILE* 3.8 2.0 - - - +
101B VAL* 4.4 0.2 - - + -
102B ALA* 1.3 75.6 - - - +
104B THR* 1.3 60.1 - - - +
105B SER 3.0 8.3 + - - +
108B ALA* 4.2 3.4 - - + -
109B ALA* 4.0 26.2 - - - +
----------------------------------------------------------
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