Contacts of the strand formed by residues 102 - 109 (chain A) in PDB entry 1JEY
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 ILE 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.9 22.0 - - + -
87A PHE 3.4 4.3 - - - +
88A TYR* 4.4 1.1 - - + -
90A THR* 4.0 0.2 + - - -
93A ASP* 3.1 4.7 - - - +
94A LYS 2.7 29.8 + - - -
95A ASN* 3.3 12.9 + - - +
99A PHE* 3.9 9.6 - - + +
100A LYS 3.3 7.1 - - - +
101A ASN* 1.3 84.5 - - - +
103A TYR* 1.3 56.8 + - - +
104A VAL* 4.9 0.4 - - + -
141A TYR* 5.8 0.9 - - + -
142A SER 6.0 0.4 - - - +
145A GLU* 3.5 19.7 - - + +
146A VAL* 3.4 50.5 - - + +
149A VAL* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.4 1.3 - - - -
87A PHE* 2.6 39.1 + - + +
90A THR* 3.9 9.1 + - - +
92A LYS* 3.7 37.6 + - + +
93A ASP 4.6 0.7 - - - -
94A LYS* 3.9 39.2 + - + +
102A ILE* 1.3 72.8 - - - +
104A VAL* 1.3 65.0 + - - +
105A LEU* 3.1 29.0 + - + -
134A MET* 4.7 11.6 + - - +
135A MET* 3.6 50.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL 3.9 2.5 - - - -
86A VAL* 4.2 13.2 - - + -
94A LYS* 2.9 42.0 + - + +
95A ASN* 4.1 5.6 - - + -
102A ILE* 4.9 0.7 - - + -
103A TYR* 1.3 73.6 - - - +
105A LEU* 1.3 61.8 + - - +
106A GLN 4.0 4.3 - - - +
107A GLU* 3.9 37.2 - - + +
149A VAL* 3.7 29.6 - - + -
153A LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 2.9 35.3 + - + +
87A PHE* 3.7 15.9 - - + -
94A LYS* 5.6 2.8 + - - -
103A TYR* 3.1 16.2 + - + -
104A VAL* 1.3 74.8 - - - +
106A GLN* 1.3 72.4 + - + +
118A GLU* 3.9 26.8 - - - +
119A LEU* 3.9 19.3 - - + -
122A PHE* 3.9 20.6 - - + -
134A MET* 4.7 4.5 - - - -
135A MET* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 2.7 40.0 + - - +
84A ALA* 3.1 4.2 - - - +
85A VAL* 2.8 41.7 + - + +
104A VAL* 4.0 5.0 - - - +
105A LEU* 1.3 86.7 - - + +
107A GLU* 1.3 64.2 + - - +
115A ARG* 3.1 55.5 + - + +
118A GLU* 2.9 30.8 + - - +
119A LEU* 3.9 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU 3.2 1.4 - - - +
84A ALA* 4.6 0.2 - - - -
104A VAL* 3.9 19.9 - - + +
105A LEU 4.3 0.2 - - - -
106A GLN* 1.3 73.8 - - - +
108A LEU* 1.3 64.7 + - - +
115A ARG* 2.5 38.7 + - - +
153A LEU* 4.0 16.7 - - + +
156A ASP* 5.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 3.9 9.6 - - - +
38A LEU 3.8 11.7 - - - +
39A ILE* 4.3 3.8 - - + -
82A LEU* 3.4 44.2 - - + +
83A LEU 3.4 2.0 - - - -
84A ALA* 3.6 23.3 - - + +
107A GLU* 1.3 75.7 - - - +
109A ASP* 1.3 62.7 + - - +
153A LEU* 3.4 35.0 - - + +
154A PHE* 3.6 31.4 - - + -
157A VAL* 5.1 7.9 - - + +
158A GLN* 5.3 5.0 - - - +
159A PHE* 5.4 2.1 - - - -
161A MET* 4.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.8 16.0 - - - +
83A LEU* 2.9 29.1 + - - +
107A GLU* 3.1 0.6 + - + -
108A LEU* 1.3 77.2 - - - +
110A ASN* 1.3 101.1 + - - +
111A PRO 3.6 0.7 - - - -
115A ARG* 3.3 27.4 + - - +
159A PHE* 4.6 10.3 - - - -
318B SER* 5.3 3.4 + - - -
----------------------------------------------------------
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