Contacts of the strand formed by residues 104 - 108 (chain A) in PDB entry 1R1P
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 104 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.8 47.5 - - + +
74A LEU* 3.6 33.0 - - + -
75A MET* 3.8 15.7 - - - -
97A SER* 4.3 0.2 - - - -
98A VAL 3.5 22.0 - - - +
99A ARG* 3.8 7.9 - - - -
103A ASP* 1.3 83.5 - - - +
105A GLN* 1.3 70.2 + - - +
106A HIS* 4.0 16.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE 3.8 0.9 - - - +
97A SER* 3.4 2.3 - - - -
98A VAL* 2.8 35.2 + - - +
100A HIS* 3.7 30.6 - - + +
103A ASP* 2.9 30.1 + - - +
104A VAL* 1.3 77.6 - - - +
106A HIS* 1.3 65.9 + - - +
107A PHE* 4.2 2.9 - - - -
143A LYS* 4.4 7.9 - - - +
559E VAL* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 3.3 59.0 - - + +
71A GLU* 2.8 42.6 + - + +
85A ARG* 3.2 7.5 + - - +
96A ILE 3.4 4.3 - - - +
97A SER* 2.8 34.3 + - - -
104A VAL* 4.0 7.9 + - + -
105A GLN* 1.3 79.5 - - - +
107A PHE* 1.3 63.3 + - - +
557E ASP 4.3 2.0 + - - +
558E PTR 3.3 16.9 - - + -
559E VAL* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 3.3 7.4 - - - -
96A ILE* 2.8 49.0 + - + +
98A VAL* 3.8 24.7 - - + -
100A HIS* 4.0 20.6 - + - -
105A GLN 4.3 2.5 - - - -
106A HIS* 1.3 77.8 - - - +
108A LYS* 1.3 58.7 + - - +
109A VAL 3.9 0.2 + - - -
119A LEU* 4.3 16.8 - - + -
120A TRP* 4.0 3.6 - + - -
139A ILE* 3.2 50.7 - - + -
140A SER* 4.6 0.7 - - - -
558E PTR 3.6 4.7 - - - -
559E VAL* 3.5 38.6 - - + -
560E ASN* 3.4 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 4.7 1.0 + - - -
89A SER* 5.3 0.2 + - - -
90A SER* 3.8 16.5 + - - -
93A ASP* 2.9 34.7 + - - +
94A PHE 3.9 6.3 - - - +
95A SER* 4.9 1.6 + - - -
107A PHE* 1.3 70.3 - - - +
109A VAL* 1.3 72.9 + - - +
110A MET* 3.1 20.3 + - + +
119A LEU* 3.8 3.7 - - - +
558E PTR 3.7 40.6 + - + -
560E ASN* 2.9 27.8 + - - -
561E VAL* 4.0 25.4 - - + -
----------------------------------------------------------
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