Contacts of the strand formed by residues 88 - 95 (chain A) in PDB entry 2JG1
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 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 3.3 50.2 + - - +
9A PRO 3.5 14.3 + - - +
10A SER* 3.4 16.2 + - - -
11A VAL* 2.9 22.7 + - - -
63A LEU* 4.0 4.7 - - - +
86A GLU 3.5 2.5 + - - -
87A THR* 1.3 78.7 - - - +
89A ASN* 1.3 61.3 + - - +
90A CYS* 3.8 18.1 - - - -
103A LEU* 4.9 6.3 - - - +
104A GLU* 2.8 47.8 + - + +
105A GLN 4.6 0.4 + - - -
106A GLY* 3.7 22.4 - - - -
107A PRO* 4.4 2.0 - - + +
33D LYS* 4.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 4.5 0.2 - - - -
11A VAL* 3.0 37.1 + - - +
13A ILE* 3.6 21.7 - - - +
63A LEU* 3.3 15.5 - - - +
88A ARG* 1.3 74.7 - - - +
90A CYS* 1.3 70.5 + - - +
91A ILE* 4.5 5.6 - - + -
104A GLU* 2.9 43.3 + - - +
13D ILE* 3.5 14.0 - - - +
15D TYR* 4.2 6.1 - - - +
33D LYS* 2.9 20.0 + - - +
89D ASN* 5.0 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.9 13.5 - - - -
11A VAL 3.0 7.2 + - - +
12A ASP* 3.4 17.3 - - - +
13A ILE 2.8 30.8 + - - +
88A ARG* 3.8 28.0 - - - -
89A ASN* 1.3 79.9 - - - +
91A ILE* 1.3 62.8 + - - +
102A ILE 3.5 7.9 - - - +
103A LEU* 3.9 28.9 - - + -
104A GLU 4.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.5 29.4 - - + -
15A TYR* 3.7 26.2 - - + -
89A ASN* 4.5 3.1 - - + -
90A CYS* 1.3 80.6 - - - +
92A ALA* 1.3 63.9 + - - +
93A ILE* 4.1 18.2 - - + -
100A THR 5.4 0.2 - - - +
101A GLU* 3.2 8.4 - - - +
102A ILE* 2.9 46.0 + - + +
103A LEU* 4.7 1.7 - - - +
13D ILE* 4.9 0.2 - - + -
15D TYR* 3.3 39.7 - - + +
91D ILE* 4.1 18.8 - - + -
102D ILE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE 2.8 13.6 + - - +
14A SER* 3.4 9.9 + - - +
15A TYR* 2.8 31.9 + - - +
91A ILE* 1.3 74.8 - - - +
93A ILE* 1.3 58.9 + - - +
94A LEU* 3.9 14.5 + - + -
99A GLN* 4.7 5.8 - - + +
100A THR 3.6 3.8 - - - -
101A GLU* 4.3 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR* 3.5 6.7 - - + +
17A LEU* 3.8 29.8 - - + -
20A LEU* 4.2 13.2 - - + -
91A ILE* 4.1 14.8 - - + -
92A ALA* 1.3 73.9 - - - +
94A LEU* 1.3 62.2 + - - +
95A HIS* 3.3 26.2 - - + -
99A GLN* 3.4 3.3 - - - -
100A THR* 2.7 55.3 + - + +
102A ILE* 5.2 4.7 - - + -
20D LEU* 5.8 0.4 - - + -
93D ILE* 4.2 20.9 - - + -
102D ILE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.5 25.1 - - - +
15A TYR 2.8 12.6 + - - +
16A PRO* 3.5 14.8 - - + +
17A LEU 2.8 29.6 + - - +
92A ALA* 4.6 8.3 - - + +
93A ILE* 1.3 71.1 - - - +
95A HIS* 1.3 60.9 + - - +
98A GLN 3.5 4.5 - - - +
99A GLN* 3.7 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.5 17.3 - - + +
20A LEU* 3.6 34.6 - - + +
93A ILE* 3.3 31.6 - - + -
94A LEU* 1.3 75.1 - - - +
96A GLU* 1.3 86.0 + - + +
97A GLY 3.2 2.2 - - - +
98A GLN* 2.8 59.4 + - - +
100A THR* 2.7 26.4 + - - -
22D LEU* 4.5 8.3 - - + -
----------------------------------------------------------
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