Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 4HWW
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 ILE 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.5 43.1 - - + +
7A THR 2.7 19.0 + - - +
8A ILE* 3.3 5.6 - - - +
9A GLY 2.8 23.8 + - - -
88A LYS* 3.8 2.0 - - - +
92A ARG* 1.3 70.1 - - - +
94A SER* 1.3 71.3 + - - +
270A LEU* 3.2 31.4 - - + +
271A SER* 3.5 22.4 - - - +
272A GLY* 4.1 2.9 - - - +
304A PHE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 3.5 5.6 - - - -
11A ILE* 4.4 8.3 - - - -
84A VAL* 3.8 24.2 - - - +
87A VAL* 3.3 26.0 - - - -
88A LYS* 4.0 3.9 - - - +
92A ARG 3.5 4.0 + - - -
93A ILE* 1.3 75.5 - - - +
95A LEU* 1.3 59.4 + - - +
96A VAL* 3.9 3.6 - - - +
107A SER* 5.2 2.3 + - - -
111A HIS* 5.1 1.4 + - - -
228A HIS* 5.3 0.5 - - - -
271A SER 3.5 5.1 + - - -
272A GLY* 3.6 14.7 - - - -
273A LEU* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.7 16.4 - - + -
9A GLY 2.9 10.5 + - - +
10A ILE* 3.5 21.0 - - + +
11A ILE* 2.8 28.2 + - - +
36A LEU* 4.5 2.2 - - + -
40A LEU* 4.2 12.1 - - + -
93A ILE 3.4 0.2 + - - -
94A SER* 1.3 73.1 - - - +
96A VAL* 1.3 63.8 + - - +
97A LEU* 3.7 25.2 + - + -
273A LEU* 3.5 16.6 - - + -
275A ILE* 3.9 22.2 - - + -
300A THR* 3.7 22.9 - - + -
304A PHE* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.4 11.9 - - + +
13A ALA* 4.1 23.8 - - + -
80A LEU* 4.0 19.7 - - + -
84A VAL* 3.9 20.9 - - + -
94A SER* 4.9 3.1 - - - -
95A LEU* 1.3 76.5 - - - +
97A LEU* 1.3 65.5 + - - +
98A GLY 3.7 0.3 + - - -
107A SER* 3.9 19.5 - - - +
273A LEU 2.9 10.0 + - - +
274A ASP* 3.7 14.6 - - - +
275A ILE* 2.9 30.0 + - - +
276A MET* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.1 19.5 - - + -
11A ILE 3.0 12.1 + - - +
12A GLY* 4.5 0.9 - - - -
13A ALA* 2.8 29.3 + - - -
28A PRO* 3.5 36.6 - - + +
31A LEU* 4.2 17.9 - - + -
32A ARG* 4.4 13.2 - - + +
36A LEU* 3.9 28.0 - - + -
37A LEU* 5.4 0.2 - - + -
95A LEU* 3.7 28.9 - - + +
96A VAL* 1.3 73.0 - - - +
98A GLY* 1.3 63.1 + - - +
275A ILE* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 3.8 2.9 - - - -
27A GLY* 3.3 25.3 - - - -
28A PRO* 3.3 5.5 - - - +
31A LEU* 4.7 2.6 - - - +
97A LEU* 1.3 76.6 - - - +
99A GLY* 1.3 70.5 + - - -
103A LEU* 4.5 0.7 - - - -
275A ILE 3.0 19.0 + - - +
276A MET* 3.7 15.0 - - - -
277A GLU 4.8 2.0 - - - -
278A VAL* 4.8 4.3 + - - +
----------------------------------------------------------
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