Contacts of the strand formed by residues 94 - 99 (chain B) 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 PHE 94 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 4.1 19.5 - - + -
92A GLY* 3.3 46.9 - - - -
93A ASP 4.2 1.6 - - - -
94A PHE* 3.3 30.1 - + - -
61B PHE* 4.0 22.2 - + - -
63B GLU* 4.7 4.5 - - + -
84B ILE* 4.0 17.3 - - + -
85B ARG 3.4 18.2 - - - -
86B ALA* 3.9 13.0 - - + -
92B GLY 4.9 0.7 - - - -
93B ASP* 1.3 82.8 - - - +
95B SER* 1.3 62.0 + - - +
108B LYS* 4.0 1.9 - - - +
109B VAL* 3.0 46.5 + - + +
127B LEU* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE 3.7 0.9 - - - +
84B ILE* 3.3 5.4 - - - +
85B ARG* 2.8 64.3 + - - +
87B SER* 3.6 6.5 - - - -
94B PHE* 1.3 75.8 + - - +
96B ILE* 1.3 64.1 + - - +
97B SER 4.0 0.4 - - - -
107B PHE 3.3 10.1 - - - -
108B LYS* 5.0 0.7 + - - -
109B VAL* 4.6 0.7 - - - -
558F PTR 2.7 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 4.2 17.5 - - + -
83B ILE 3.4 8.3 - - - +
84B ILE* 3.9 21.1 - - + -
95B SER* 1.3 77.2 - - - +
97B SER* 1.3 62.2 + - - +
98B VAL* 3.8 19.3 - - + -
106B HIS* 3.3 2.7 - - - -
107B PHE* 2.8 50.7 + - + +
109B VAL* 3.7 24.7 - - + -
119B LEU* 4.1 12.8 - - + -
127B LEU* 5.1 0.7 - - + -
130B LEU* 3.9 25.8 - - + -
131B VAL* 5.5 2.0 - - + -
139B ILE* 4.7 6.3 - - + -
147B LEU* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.7 9.1 - - - +
74B LEU* 3.4 18.5 - - - +
82B PHE* 3.1 7.6 - - - +
83B ILE* 2.9 34.5 + - - -
85B ARG* 3.0 20.1 + - - -
95B SER 4.0 0.6 - - - -
96B ILE* 1.3 73.2 - - - +
98B VAL* 1.4 60.5 + - - +
104B VAL* 4.0 2.5 - - - -
105B GLN 3.4 4.5 - - - -
106B HIS* 2.7 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 4.4 2.7 - - - -
81B PHE 3.7 7.2 - - - +
82B PHE* 4.1 0.2 - - + -
96B ILE* 3.8 19.7 - - + -
97B SER* 1.4 79.9 - - - +
99B ARG* 1.3 70.0 + - - +
100B HIS* 2.9 30.7 + - + -
104B VAL* 3.5 4.6 - - - +
105B GLN 2.8 23.6 + - - +
107B PHE* 3.7 19.3 - - + -
139B ILE* 4.2 4.9 - - + -
145B VAL* 4.0 20.9 - - + -
147B LEU* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.1 34.9 + - + +
75B MET* 3.0 41.5 + - - +
77B LYS 3.2 13.8 + - - +
78B ASP 3.3 31.4 - - - +
79B ILE* 3.5 5.5 - - - +
80B GLY* 2.8 27.1 + - - +
81B PHE* 3.0 15.3 + - - +
98B VAL* 1.3 73.0 - - - +
100B HIS* 1.3 71.6 + - - +
101B GLU 2.9 29.4 + - - -
102B ASP* 3.7 0.8 - - - +
103B ASP 3.6 16.6 - - - +
104B VAL* 4.0 8.7 - - - -
145B VAL* 4.1 0.9 - - - +
----------------------------------------------------------
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