Contacts of the strand formed by residues 63 - 71 (chain A) in PDB entry 3RRQ
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 63 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.6 43.7 - + + -
57A SER* 5.6 0.2 - - - -
58A ASN* 4.0 29.6 - - + +
62A SER* 1.3 82.4 - - - +
64A VAL* 1.3 75.3 + - - +
65A LEU* 4.3 11.0 - - + -
82A PHE* 4.3 17.5 - + - +
83A PRO* 4.5 7.6 - - - +
99A GLN* 5.2 2.7 - - - -
103A GLY 5.0 4.3 - - - -
106A PHE* 3.9 30.7 - + - -
125A ALA* 4.9 0.4 - - + -
126A ILE 3.2 15.9 - - - +
127A SER* 5.1 0.2 - - - -
128A LEU* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 1.3 76.0 - - - +
65A LEU* 1.3 61.2 + - - +
66A ASN* 3.1 28.5 - - - +
81A ALA* 4.7 4.7 - - + -
82A PHE 3.6 13.5 - - - +
83A PRO* 5.0 7.6 - - + -
124A GLY 3.8 1.0 - - - +
125A ALA* 3.3 3.3 - - - +
126A ILE* 2.7 50.5 + - + +
128A LEU* 6.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 5.1 2.5 - - + -
54A CYS* 3.8 28.7 - - - -
56A PHE* 5.1 5.2 - - + -
63A PHE* 4.2 18.8 - - + -
64A VAL* 1.3 71.6 - - - +
66A ASN* 1.3 62.0 + - - +
67A TRP 4.3 0.2 + - - -
81A ALA* 3.5 3.1 - - - -
82A PHE* 3.0 40.6 + - + +
97A VAL* 5.1 0.3 - - - +
106A PHE* 3.4 44.4 - - + -
108A MET* 4.1 13.9 - - + +
123A CYS* 4.4 2.5 - - + -
124A GLY 3.2 25.8 - - - +
125A ALA* 4.0 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.1 25.4 - - - +
65A LEU* 1.3 72.8 - - - +
67A TRP* 1.3 61.1 + - - +
68A TYR* 2.7 41.7 + - + -
78A LYS* 3.9 22.6 + - + +
80A ALA 3.9 2.5 - - - -
81A ALA* 3.4 12.1 - - - +
108A MET* 4.9 1.3 - - - -
122A LEU 3.9 0.2 - - - +
123A CYS* 3.2 7.4 - - - +
124A GLY 2.7 40.6 + - - +
126A ILE* 4.2 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.5 21.8 - + - -
52A PHE* 4.3 9.4 - + - -
65A LEU 4.3 0.2 + - - -
66A ASN* 1.3 72.9 - - - +
68A TYR* 1.3 67.5 + - - +
78A LYS* 3.7 3.5 - - - +
79A LEU* 2.8 44.4 + - + +
80A ALA* 3.0 32.1 + - + +
95A PHE* 3.7 19.1 - + + -
96A ARG 3.8 2.9 - - - -
97A VAL* 4.1 3.6 - - + -
108A MET* 3.4 37.9 - - + -
109A SER 3.5 45.8 - - - -
110A VAL* 3.7 19.7 - - + -
121A TYR* 3.5 19.4 - + - +
122A LEU 3.5 14.6 - - - -
123A CYS* 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 2.7 46.7 + - + -
67A TRP* 1.3 74.5 - - - +
69A ARG* 1.3 59.3 + - - +
70A MET* 3.9 21.8 - - - -
77A ASP 3.4 4.3 - - - +
78A LYS* 3.6 35.4 - - + +
79A LEU* 4.4 0.7 - - - -
121A TYR* 3.2 9.9 - - - +
122A LEU* 2.9 52.5 + - + +
124A GLY* 4.5 9.4 - - - -
126A ILE* 4.6 8.3 - - - +
134A ILE* 4.6 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 1.3 72.9 - - - +
70A MET* 1.3 64.3 + - - +
71A SER 3.1 18.8 + - - +
72A PRO* 3.3 16.3 - - - +
75A GLN* 3.6 41.0 + - - +
76A THR* 3.1 21.0 - - - -
77A ASP 2.8 18.3 + - - +
79A LEU* 4.0 15.8 - - + +
95A PHE* 5.9 3.0 - - - -
116A ASN 2.8 26.4 + - - -
117A ASP* 3.6 8.5 + - - +
118A SER 2.6 28.8 + - - -
120A THR 3.9 1.3 - - - +
121A TYR* 3.6 42.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.9 23.1 - - - -
69A ARG* 1.3 75.0 - - - +
71A SER* 1.3 63.3 + - - +
72A PRO 4.4 0.7 - - - -
73A SER* 4.6 1.4 - - - -
76A THR* 3.1 23.9 - - + +
120A THR 2.8 11.1 + - - +
122A LEU* 3.9 36.1 - - + +
136A GLU* 5.7 1.6 - - - +
139A ARG* 3.4 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.1 20.4 + - - +
70A MET* 1.3 81.6 - - - +
72A PRO* 1.4 76.5 + - - +
73A SER* 4.4 1.8 - - - -
119A GLY* 3.4 4.6 - - - -
120A THR* 2.9 44.5 + - - +
139A ARG* 4.1 6.3 - - - -
----------------------------------------------------------
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