Contacts of the strand formed by residues 88 - 92 (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 HIS 88 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLY* 2.8 32.3 + - - +
42F THR* 3.5 11.9 - - - +
43F LYS* 3.4 43.4 + - + +
46F PRO* 3.6 9.3 - - + +
47F ASN* 2.9 32.5 + - - +
79F ALA* 4.2 15.3 + - + +
80F GLN 3.4 5.4 - - - +
81F ARG* 3.4 45.1 + - + +
86F GLY 3.5 9.4 - - - -
87F THR* 1.3 72.6 - - - +
89F TYR* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A TYR* 4.0 5.4 - + - -
512A ASN* 3.4 30.3 + - - +
514A LYS* 4.0 4.0 + - - -
46F PRO* 4.4 0.7 - - - -
47F ASN* 3.2 20.2 - - + +
49F VAL* 4.0 10.8 - - + -
58F VAL* 3.7 24.5 - - + -
59F GLY 4.8 1.0 + - - -
60F CYS* 3.1 34.2 - - - +
72F PHE* 3.7 24.2 - + + -
74F LEU* 3.6 24.2 - - + +
79F ALA* 3.3 3.3 - - - -
80F GLN 2.9 33.1 + - - +
82F CYS* 4.3 1.8 - - + -
87F THR* 3.2 33.7 + - - -
88F HIS* 1.3 72.7 - - - +
90F LYS* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F PRO* 4.0 26.9 - - + -
47F ASN 2.8 9.8 + - - +
48F LEU* 3.4 16.0 - - + -
49F VAL 2.8 24.4 + - - -
74F LEU* 3.8 5.1 - - - +
77F GLY 2.9 31.7 + - - +
78F GLU* 4.7 5.8 + - - +
79F ALA* 4.2 17.9 - - + +
89F TYR* 1.3 76.0 - - - +
91F LEU* 1.3 73.3 + - - +
92F VAL* 4.0 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F VAL* 3.4 9.2 - - + +
51F SER* 3.7 19.7 - - - -
53F THR 3.6 4.0 - - - +
54F ASN* 3.6 33.0 - - - +
55F LYS 3.9 0.4 - - - +
56F ARG* 4.0 12.6 - - + +
74F LEU* 3.6 35.6 - - + +
75F HIS 3.9 15.7 + - - +
76F LYS* 3.9 8.6 - - - +
77F GLY 5.2 4.0 + - - +
90F LYS* 1.3 86.6 + - - +
92F VAL* 1.3 69.0 + - - +
93F PRO* 3.5 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LEU* 3.8 34.8 - - + -
49F VAL 2.8 24.3 + - - +
50F PRO* 3.8 6.7 - - + -
51F SER 3.2 16.7 + - - -
90F LYS* 4.0 4.5 - - + +
91F LEU* 1.3 79.9 - - - +
93F PRO* 1.3 69.5 - - - +
95F GLN* 3.0 41.9 - - + +
----------------------------------------------------------
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