Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 4JCQ
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 81 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 5.0 1.1 - - + -
53A ILE* 3.4 12.1 - - + +
55A ILE* 3.6 31.2 - - + -
74A ILE* 3.8 34.5 - - + +
77A ILE* 3.9 21.8 - - + -
79A PRO 3.5 10.7 + - - +
80A THR* 1.3 78.1 - - - +
82A LYS* 1.3 71.8 + - - +
83A VAL* 4.3 6.1 - - + -
100A ALA* 3.5 19.7 - - + +
101A GLU 4.9 0.2 + - - -
104A ASN* 3.6 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 4.0 26.8 - - + +
53A ILE 2.8 11.5 + - - +
54A THR* 3.4 16.3 - - + +
55A ILE 2.8 31.5 + - - -
80A THR* 4.9 8.4 - - + +
81A VAL* 1.3 77.6 - - - +
83A VAL* 1.3 58.7 + - - +
104A ASN* 3.5 31.1 + - + +
106A PHE* 4.1 22.7 - - + -
189A LEU* 4.3 17.5 - - + +
190A LYS 4.5 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.3 15.0 - - + +
57A ILE* 4.0 18.6 - - + -
74A ILE* 5.2 2.9 - - + -
81A VAL* 4.2 7.8 + - + -
82A LYS* 1.3 79.2 - - - +
84A VAL* 1.3 58.7 + - - +
96A ILE 4.8 3.6 - - - +
97A TYR* 3.4 46.0 - - + +
100A ALA* 3.8 21.8 - - + +
104A ASN 3.0 7.8 + - - +
105A ARG* 3.8 12.3 - - + -
106A PHE* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 3.9 23.8 - - + -
55A ILE 2.7 10.0 + - - +
56A PHE* 3.3 29.1 - - + -
57A ILE 2.9 25.4 + - - -
82A LYS 5.4 0.2 - - - -
83A VAL* 1.3 77.7 - - - +
85A GLY* 1.3 66.6 + - - +
86A THR* 3.7 1.9 + - - +
97A TYR* 4.4 1.6 - - - -
106A PHE* 3.4 7.4 - - + +
107A SER* 4.5 2.7 - - - -
108A LEU* 3.7 35.0 - - + +
183A ILE* 4.6 5.4 - - + -
189A LEU* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE 3.6 7.2 - - - -
84A VAL* 1.3 72.2 - - - +
86A THR* 1.3 60.3 + - - -
89A VAL* 3.9 11.0 - - - -
97A TYR* 3.6 8.3 - - - -
106A PHE 3.0 12.9 + - - -
107A SER* 3.5 0.7 + - - -
108A LEU* 2.9 27.0 + - - +
111A THR* 3.4 8.9 + - - -
113A TYR* 3.4 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 4.2 9.2 - - - +
56A PHE* 4.5 6.5 - - + -
57A ILE 2.9 23.7 + - - +
58A ASN* 3.2 25.4 - - + +
84A VAL 4.1 5.8 - - - +
85A GLY* 1.3 76.1 - - - -
87A GLY* 1.3 61.7 + - - +
88A TRP 3.0 8.4 + - - -
108A LEU* 3.8 24.8 - - + +
111A THR* 3.3 9.3 - - - +
68G ASP 4.8 0.5 + - - -
69G THR* 2.7 44.3 + - + +
72G ASP* 4.9 0.9 + - - +
73G MET* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 3.8 1.3 - - - -
86A THR* 1.3 71.5 + - - +
88A TRP* 1.3 62.5 + - - +
110A ASN 3.3 19.2 + - - +
111A THR* 3.2 6.4 + - - -
112A ARG* 3.2 22.9 + - - +
65G GLU* 3.5 32.3 - - - +
68G ASP* 4.2 6.8 - - - +
69G THR* 3.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 3.1 18.1 + - - -
59A SER 2.8 33.8 + - - -
60A GLN* 3.6 35.4 - - + +
86A THR 3.0 3.4 + - - -
87A GLY* 1.3 75.5 - - - +
89A VAL* 1.3 68.1 + - - +
111A THR* 4.1 1.3 - - - -
112A ARG* 3.3 43.3 - - + +
167A TRP* 3.6 34.8 - + + -
32G GLN* 3.4 19.6 - - - +
65G GLU* 3.5 34.9 - - + +
131G ILE* 4.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.6 25.1 - - + +
59A SER 3.4 3.8 - - - +
85A GLY* 3.9 13.2 - - - -
88A TRP* 1.3 79.6 - - - +
90A ALA* 1.3 60.4 + - - +
93A GLY* 3.5 30.3 - - - +
94A ILE* 3.5 17.7 - - + +
97A TYR* 3.9 13.5 - - + -
111A THR* 4.3 2.5 - - + -
112A ARG 3.0 6.2 + - - -
113A TYR* 3.3 31.3 - - + -
114A MET 3.1 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER 2.9 7.7 + - - +
60A GLN* 3.7 16.8 - - - +
61A GLY* 3.4 9.9 + - - -
89A VAL* 1.3 77.4 - - - +
91A SER* 1.3 64.1 + - - +
92A ALA 3.2 0.9 + - - -
93A GLY* 2.8 24.8 + - - -
94A ILE* 3.8 3.4 - - - -
114A MET* 3.2 19.3 - - + +
167A TRP* 3.7 26.9 - - + -
----------------------------------------------------------
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