Contacts of the strand formed by residues 91 - 96 (chain A) in PDB entry 4ARH
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 VAL 91 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.3 0.4 - - - +
86A GLY 3.6 1.7 - - - +
87A ILE* 3.4 5.5 - - - +
88A GLU 2.8 35.0 + - - +
89A ASN* 3.8 9.9 - - + +
90A GLY* 1.3 83.6 - - - +
92A ILE* 1.3 66.3 + - - +
93A GLU* 4.1 2.8 + - + +
102A SER* 3.8 24.7 - - - +
103A CYS 3.4 10.8 - - - +
104A LYS* 3.9 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.1 24.7 - - + -
85A ILE* 3.8 21.5 - - + -
86A GLY 3.4 3.1 - - - +
87A ILE* 4.1 12.6 - - + -
91A VAL* 1.3 78.1 - - - +
93A GLU* 1.3 61.7 + - - +
94A PHE* 3.2 33.5 - - + -
102A SER* 3.2 21.5 - - - -
103A CYS 3.1 10.1 + - - -
105A TYR* 3.5 39.7 - - + -
126A PHE* 5.2 0.9 - - + -
139A VAL* 4.3 11.7 - - + -
141A PHE* 4.2 13.2 - - + -
156A ILE* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 5.1 6.2 - - - +
84A THR 3.9 0.2 - - - +
85A ILE* 3.2 10.2 - - - +
86A GLY* 2.8 44.5 + - - +
91A VAL* 4.1 3.7 - - + -
92A ILE* 1.3 74.3 - - - +
94A PHE* 1.3 61.2 + - - +
95A HIS* 2.8 34.1 + - + +
100A VAL* 4.1 16.6 - - + +
101A ALA 3.4 6.7 - - - +
102A SER* 3.9 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.2 9.6 - - + -
84A THR 3.8 3.4 - - - -
85A ILE* 4.1 19.5 - - + -
92A ILE* 3.2 38.6 - - + -
93A GLU* 1.3 72.9 - - - +
95A HIS* 1.3 61.7 + - - +
96A ARG 3.8 0.2 - - - -
100A VAL* 3.3 6.1 - - - -
101A ALA 2.7 39.3 + - - +
105A TYR* 3.3 27.8 - + - -
135A ALA* 4.0 5.6 - - + -
136A PRO* 3.6 20.0 - - + -
139A VAL* 4.1 9.2 - - + -
156A ILE* 4.4 4.9 - - + -
158A MET* 3.6 31.6 - - - -
1197A SO4 3.6 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 5.8 3.0 - - - +
82A VAL* 3.3 4.7 - - - -
83A GLU* 3.0 28.5 + - + +
84A THR* 2.9 49.2 + - + +
85A ILE* 5.1 0.2 - - - -
86A GLY 5.1 0.4 - - - -
93A GLU* 2.8 36.5 + - + -
94A PHE* 1.3 75.3 - - - +
96A ARG* 1.3 58.2 + - - +
97A ASP 3.9 6.3 - - - +
99A ASN 3.5 5.6 - - - +
100A VAL* 4.0 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.4 34.1 - - + +
82A VAL* 4.0 8.3 - - + +
94A PHE 3.7 1.2 + - - -
95A HIS* 1.3 70.5 - - - +
97A ASP* 1.3 70.0 + - + +
98A ASN 3.1 0.5 + - - -
99A ASN* 2.8 39.3 + - + +
1194A SO4 3.3 38.2 + - - -
1197A SO4 3.1 36.1 - - - +
----------------------------------------------------------
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