Contacts of the strand formed by residues 91 - 100 (chain A) in PDB entry 1W1W
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 91 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 5.1 0.7 + - - -
11A ASN* 3.9 20.3 + - - +
66A ILE* 3.6 7.1 - - - +
89A PRO* 3.4 1.6 - - - +
90A GLN* 1.3 81.3 + - - +
92A ALA* 1.3 63.6 + - - +
93A TYR* 6.1 1.0 - - - -
110A ILE* 4.5 12.1 - - - +
111A ILE 3.2 15.3 - - - -
112A SER* 4.1 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.2 7.4 - - - +
11A ASN 3.3 26.7 - - - +
12A PHE* 4.2 7.9 - - + +
48A PHE* 5.6 0.2 - - - -
66A ILE* 3.7 22.0 - - + +
91A SER* 1.3 76.4 - - - +
93A TYR* 1.3 61.6 + - - +
110A ILE* 3.4 3.9 - - - +
111A ILE* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 2.8 33.2 + - + +
9A LEU* 4.4 0.2 - - - +
10A SER* 3.0 62.6 + - - +
12A PHE* 4.7 1.4 - - - +
18A VAL* 4.4 11.6 - - + +
48A PHE* 5.0 0.9 - - - -
91A SER* 6.1 1.1 - - - -
92A ALA* 1.3 77.6 - - - +
94A VAL* 1.3 76.8 + - - +
95A LYS* 3.5 35.1 + - + -
108A MET* 4.3 9.4 - - + -
109A ARG 3.1 14.4 - - - +
110A ILE* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.8 3.1 - - + -
8A GLU 3.3 4.5 - - - -
9A LEU* 3.5 23.3 - - + -
12A PHE* 3.5 33.4 - - + -
45A ALA* 3.7 15.7 - - + +
48A PHE* 3.7 15.0 - - + -
49A VAL* 3.0 38.2 - - + +
93A TYR* 1.3 81.8 - - - +
95A LYS* 1.3 70.1 + - - +
108A MET* 3.2 2.1 - - - +
109A ARG 3.0 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.0 11.5 - - - +
8A GLU* 2.8 69.2 + - + +
49A VAL* 4.1 2.5 - - - -
93A TYR* 3.5 21.2 + - + -
94A VAL* 1.3 78.4 - - - +
96A ALA* 1.3 60.4 + - - +
97A PHE* 4.2 11.2 - - + -
106A GLU* 3.0 30.7 + - - +
107A LEU 3.1 5.2 - - - +
108A MET* 3.3 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.4 8.5 - - + -
6A GLY 3.7 4.7 - - - -
7A LEU* 4.1 9.0 - - + -
49A VAL* 4.0 23.5 - - + +
50A LEU* 5.3 4.0 - - + -
95A LYS* 1.3 75.6 - - - +
97A PHE* 1.3 63.3 + - - +
98A TYR* 3.7 2.0 + - + +
105A VAL 3.5 1.2 - - - +
106A GLU* 3.3 4.7 - - - +
107A LEU* 2.7 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.9 2.6 - - - +
5A VAL* 2.9 35.0 + - + +
6A GLY* 3.0 32.7 + - - +
7A LEU* 4.2 5.6 - - - -
8A GLU* 4.1 29.8 - - + -
95A LYS* 4.2 20.9 - - + -
96A ALA* 1.3 70.9 - - - +
98A TYR* 1.3 59.9 + - - +
104A LEU* 3.5 26.9 - - + -
105A VAL 3.4 4.0 - - - -
106A GLU* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY* 3.1 41.9 + - - -
3A ARG 3.4 10.3 - - - -
4A LEU* 4.9 3.4 - - + +
96A ALA* 3.7 2.6 - - + +
97A PHE* 1.3 74.3 - - - +
99A GLN* 1.3 58.9 + - - +
100A LYS* 3.5 16.2 + - + -
104A LEU* 3.0 5.1 - - - +
105A VAL* 2.8 47.0 + - + +
107A LEU* 4.7 14.4 - - + -
134A PHE* 4.3 13.2 - + - -
138A GLU* 2.8 49.6 + - + +
140A ILE* 3.9 19.7 - - + -
1152A PRO* 3.6 11.2 - - + +
1153A PHE* 4.1 15.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY* 2.8 23.7 - - - -
3A ARG* 2.8 32.8 + - + +
5A VAL* 4.0 22.4 - - + +
97A PHE 3.9 0.2 + - - -
98A TYR* 1.3 72.7 - - - +
100A LYS* 1.3 55.7 + - - +
101A GLY 3.5 17.9 + - - +
102A ASN 4.1 3.5 - - - +
103A LYS 3.3 19.6 - - - +
104A LEU* 3.9 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY* 4.8 1.3 - - - -
98A TYR* 3.5 12.5 + - + -
99A GLN* 1.3 69.9 - - - +
101A GLY* 1.3 60.3 + - - +
102A ASN 3.5 0.2 + - - -
103A LYS* 3.1 50.5 + - - +
105A VAL* 4.0 12.6 - - + -
134A PHE* 3.9 25.1 - - + -
137A ASN* 4.2 14.3 + - - +
138A GLU* 2.5 49.9 + - - +
----------------------------------------------------------
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