Contacts of the strand formed by residues 74 - 79 (chain B) in PDB entry 1RXV
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 ARG 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY* 5.8 2.7 - - - -
22B LYS 3.2 16.1 + - - +
23B LYS* 3.2 14.4 - - + +
24B ILE 3.0 22.6 + - - -
69B VAL* 3.2 42.5 + - - +
72B GLY* 3.3 24.0 + - - -
73B ILE* 1.3 81.1 + - - +
75B PRO* 1.3 60.9 - - - +
76B VAL* 3.8 0.7 + - - +
292B PHE* 3.3 44.0 - - + +
323B LYS 4.5 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.4 9.2 - - + +
26B VAL* 4.1 19.1 - - + -
65B VAL* 4.0 26.5 - - + -
68B MET* 4.6 16.4 - - + -
69B VAL* 4.5 8.5 - - + -
73B ILE* 3.1 20.6 - - + +
74B ARG* 1.3 84.0 - - - +
76B VAL* 1.3 61.1 + - - +
77B PHE* 4.1 9.2 - - + -
143B ILE* 3.3 24.1 - - + +
144B PRO* 4.0 0.5 - - - +
292B PHE* 3.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 5.1 1.6 - - + -
24B ILE 2.7 15.3 + - - +
25B ALA* 3.3 8.1 - - - -
26B VAL 2.7 30.4 + - - +
74B ARG 4.3 3.1 - - - +
75B PRO* 1.3 76.7 - - - +
77B PHE* 1.3 64.6 + - - +
78B VAL* 3.7 1.0 + - + +
144B PRO* 3.5 16.8 - - + +
146B VAL* 4.1 18.8 - - + -
159B MET* 4.3 6.7 - - + -
165B VAL* 4.7 8.1 - - + -
290B ILE* 3.5 51.4 - - + -
292B PHE* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.4 24.5 - - + -
28B ALA* 4.2 19.3 - - + -
31B THR* 4.5 17.7 - - + -
32B LEU* 5.4 3.1 - - + -
35B PHE* 5.8 0.7 - + - -
61B ILE* 4.9 12.6 - - + -
65B VAL* 3.7 31.2 - - + -
68B MET* 5.2 3.4 - - + -
75B PRO* 4.2 18.2 - - + -
76B VAL* 1.3 77.2 - - - +
78B VAL* 1.3 55.7 + - - +
79B PHE* 3.9 11.0 - + + -
138B LEU* 3.7 35.9 - - + -
143B ILE* 4.0 15.9 - - + -
144B PRO 3.2 5.7 + - - -
145B PHE* 2.9 8.0 - - + +
146B VAL* 2.7 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 4.1 9.2 - - + -
26B VAL 2.9 15.2 + - - +
27B ASP* 4.0 2.8 - - - +
28B ALA* 3.0 23.3 + - - +
29B PHE 4.4 1.2 + - - -
76B VAL* 3.9 8.5 - - + +
77B PHE* 1.3 75.8 - - - +
79B PHE* 1.3 62.3 + - - +
80B ASP* 4.2 0.9 + - - +
146B VAL* 3.4 11.2 - - + +
148B ALA* 4.2 2.7 - - + -
152B GLY* 3.5 31.1 - - - +
155B GLN* 3.6 27.4 - - + -
156B ALA* 3.8 21.8 - - + +
159B MET* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 3.6 20.2 - - + -
29B PHE 5.5 0.7 - - - -
32B LEU* 3.9 16.6 - - + -
77B PHE* 3.9 13.2 - + + -
78B VAL* 1.3 75.2 - - - +
80B ASP* 1.3 66.7 + - - +
131B VAL* 3.6 37.2 - - + -
134B ALA* 4.2 9.2 - - + -
135B LYS* 3.7 27.8 - - + -
138B LEU* 4.0 13.7 - - + -
145B PHE* 3.7 31.4 - + + -
146B VAL 2.8 10.4 + - - +
147B ASP* 3.6 17.5 - - - +
148B ALA* 3.0 31.8 + - - +
152B GLY* 4.5 1.1 - - - -
----------------------------------------------------------
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