Contacts of the strand formed by residues 70 - 75 (chain f) in PDB entry 5W97
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 70 (chain f).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265a LYS* 4.4 18.2 - - + +
489a THR* 3.4 16.2 - - - +
490a THR* 3.9 25.1 - - + -
58f VAL 3.6 1.7 - - - +
59f GLY* 3.2 1.4 - - - -
60f CYS* 2.7 40.8 + - - +
62f CYS* 3.9 12.1 - - - -
68f THR* 4.8 4.3 - - + +
69f VAL* 1.3 72.9 - - - +
71f TRP* 1.3 62.3 + - - +
72f PHE* 4.0 4.5 - - + -
82f CYS* 3.9 20.9 - - - -
83f PRO* 4.1 18.8 - - + -
84f SER* 3.7 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 71 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86a MET 4.9 3.9 + - - -
87a ILE 5.6 0.4 - - - -
173a PRO* 4.5 1.6 - - + -
176a MET* 3.5 33.4 - - + -
488a THR* 4.3 2.6 + - - +
489a THR* 2.8 44.2 + - - +
490a THR* 4.7 3.1 - - - -
492a LEU* 3.7 46.5 - - + +
495a LEU* 3.7 22.4 - - + +
509a THR* 3.8 26.7 - - + -
511a VAL* 3.9 8.3 - - + -
57f ILE* 3.8 12.3 - - + -
58f VAL 3.2 4.5 - - - -
59f GLY* 3.1 33.4 - - - -
69f VAL* 3.6 29.9 + - + +
70f ILE* 1.3 72.8 - - - +
72f PHE* 1.3 64.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489a THR* 5.1 1.8 - - + -
495a LEU* 4.1 7.9 - - - +
57f ILE* 4.3 4.5 - - - -
58f VAL* 2.7 78.7 + - + +
60f CYS* 4.3 3.4 - - + -
70f ILE* 4.0 11.2 - - + -
71f TRP* 1.3 77.6 - - - +
73f TRP* 1.3 75.1 + - - +
74f LEU* 3.4 11.3 + - + -
80f GLN* 5.1 5.6 - - + -
81f ARG 4.6 7.6 - - - -
82f CYS* 3.8 17.0 - - + -
83f PRO* 3.5 34.5 - - + -
89f TYR* 3.8 22.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 73 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495a LEU* 2.5 41.1 + - + +
496a ASN* 3.3 29.4 - - - -
11d TYR* 4.1 11.7 - + - -
12d ALA* 3.5 46.8 - - + +
55f LYS* 3.8 34.3 - - + -
56f ARG* 3.8 19.7 - - - -
57f ILE* 3.7 32.7 - - + +
72f PHE* 1.3 81.9 - - - +
74f LEU* 1.3 59.5 + - - +
75f HIS* 3.8 8.1 - - - +
80f GLN* 3.5 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49f VAL* 3.5 41.1 - - + -
55f LYS* 3.1 5.9 - - - +
56f ARG 2.9 38.7 + - - +
58f VAL* 3.8 14.1 - - + -
72f PHE* 3.4 3.6 + - + -
73f TRP* 1.3 73.4 - - - +
75f HIS* 1.3 62.7 + - - +
78f GLU 5.3 0.2 - - - +
80f GLN* 3.6 30.3 - - + +
89f TYR* 3.4 29.8 - - + +
90f LYS* 4.9 0.2 - - - -
91f LEU* 3.6 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 75 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9d GLU 5.8 0.9 - - - -
12d ALA* 2.6 44.9 + - + -
13d LEU* 3.8 24.7 - - + +
14d PRO* 5.4 4.7 - - + -
54f ASN* 3.7 4.3 + - - +
55f LYS* 3.8 19.4 - - + +
73f TRP* 3.8 14.9 - - - +
74f LEU* 1.3 80.3 - - - +
76f LYS* 1.3 71.2 + - - +
77f GLY 3.4 2.1 + - - -
78f GLU 4.3 1.9 - - - +
80f GLN* 3.0 32.1 + - - +
91f LEU* 4.1 11.0 + - - +
----------------------------------------------------------
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