Contacts of the strand formed by residues 138 - 148 (chain S) in PDB entry 1NJI
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 SER 138 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2053A G 2.5 25.3 + - - -
22S GLN* 4.1 18.5 + - - -
121S GLU* 3.1 6.1 - - - -
122S GLN* 2.7 55.9 + - - +
136S TRP 5.1 0.9 + - - -
137S ASN* 1.3 74.5 - - - +
139S PRO* 1.3 72.5 - - - +
140S GLN* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370A G 3.4 29.6 - - + +
2053A G 4.4 9.0 - - - +
2054A A 5.6 2.0 - - - +
21S ARG 3.4 1.0 - - - +
22S GLN* 3.4 23.4 - - - +
23S MET 3.6 20.5 + - - +
25S PHE* 4.4 14.4 - - + +
118S LYS* 4.1 24.5 - - - +
120S GLY 3.7 6.3 - - - +
121S GLU* 4.5 3.1 - - + +
137S ASN 4.2 3.8 - - - +
138S SER* 1.3 88.0 - - - +
140S GLN* 1.3 60.6 + - - +
141S VAL* 4.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S GLU* 3.9 39.8 + - + +
21S ARG 3.3 3.6 - - - -
22S GLN* 4.5 15.8 - - + +
118S LYS* 3.5 5.2 - - - -
119S VAL* 2.8 29.4 + - + +
120S GLY* 2.7 22.6 + - - +
121S GLU 3.6 16.3 + - - +
122S GLN* 3.9 31.1 + - - +
138S SER 4.1 0.7 - - - +
139S PRO* 1.3 77.5 - - - +
141S VAL* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S LEU 4.2 0.7 - - - +
19S ARG* 3.5 1.7 - - - -
20S GLU 3.0 4.9 + - - -
21S ARG* 2.6 44.2 + - - +
23S MET* 3.8 42.2 - - + +
25S PHE* 3.7 37.2 - - + -
28S SER* 4.2 1.6 - - - +
116S ALA* 4.0 17.9 - - + -
117S HIS 3.6 6.1 - - - +
139S PRO* 4.8 0.2 - - + -
140S GLN* 1.3 81.9 - - - +
142S ASP* 1.3 80.2 + - - +
143S VAL* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S GLY* 3.3 7.0 - - - -
2S ILE* 3.0 43.4 + - + -
18S LEU 3.2 8.7 - - - +
19S ARG* 3.0 19.7 + - - -
20S GLU* 2.7 35.0 + - - +
117S HIS 2.9 30.8 + - - +
119S VAL* 3.1 22.0 - - + +
141S VAL* 1.3 78.8 - - - +
143S VAL* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S ILE* 4.2 5.3 - - - +
17S MET* 3.2 8.1 - - - +
18S LEU* 3.0 71.7 + - + -
23S MET* 4.9 7.4 - - + -
88S PHE* 4.2 20.0 - - + -
91S LEU* 3.7 16.0 - - + +
114S VAL* 4.4 0.9 - - + -
115S ALA 3.1 24.5 - - - +
116S ALA* 4.1 6.1 - - + +
141S VAL* 4.8 1.6 - - + -
142S ASP* 1.3 78.4 - - - +
144S GLU* 1.3 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S ILE* 3.8 19.3 - - + -
3S SER 4.4 1.0 - - - +
4S TYR* 3.3 25.2 - - + +
5S SER* 2.5 45.2 + - - -
6S VAL 4.4 0.3 + - - -
16S ALA 3.6 4.5 - - - -
17S MET* 4.0 2.7 - - + -
113S HIS* 3.1 27.3 + - + +
114S VAL* 3.2 4.8 - - - +
115S ALA* 3.0 33.3 + - - +
117S HIS* 3.1 19.2 - - + -
143S VAL* 1.3 79.6 - - - +
145S LEU* 1.3 61.7 + - - +
146S ILE* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S TYR* 4.0 0.9 - - - -
14S ALA 3.9 0.2 - - - +
15S LYS* 3.4 5.7 - - - +
16S ALA* 3.0 37.6 + - + +
35S ILE* 5.7 1.8 - - + -
91S LEU* 4.0 25.6 - - + -
92S LEU* 3.5 35.0 - - + -
95S ALA* 4.1 20.4 - - + -
111S ILE* 3.4 29.2 - - + -
113S HIS 3.0 17.9 - - - +
114S VAL* 3.8 9.4 - - + -
144S GLU* 1.3 77.2 - - - +
146S ILE* 1.3 72.0 + - - +
147S LEU* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S TYR* 4.2 22.0 - - + -
6S VAL* 4.0 33.4 - - + +
7S GLU 4.9 0.2 - - - +
8S ALA* 4.1 18.6 - - + -
13S THR* 3.7 22.4 - - + +
14S ALA 3.4 5.8 - - - +
15S LYS* 4.5 3.6 - - + -
111S ILE* 3.7 2.3 - - - -
112S LYS* 2.9 41.4 + - + +
113S HIS* 2.7 37.8 + - + +
145S LEU* 1.3 80.0 - - - +
147S LEU* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S THR* 3.2 10.6 + - - -
14S ALA* 2.7 39.0 + - + +
40S ALA* 4.1 15.3 - - + -
92S LEU* 5.1 1.1 - - + -
95S ALA* 3.6 44.4 - - + +
96S VAL* 3.9 13.7 - - + +
99S ALA* 4.4 5.4 - - + -
106S GLY 4.7 0.7 - - - +
109S MET* 3.8 21.8 - - + -
110S THR 3.2 13.5 - - - +
111S ILE* 4.1 20.9 - - + -
145S LEU* 4.7 9.6 - - + -
146S ILE* 1.3 74.5 - - - +
148S GLU* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S THR* 3.4 20.8 + - - +
13S THR* 4.3 5.5 + - - +
109S MET* 3.5 5.9 - - - +
110S THR* 2.8 41.6 + - - +
112S LYS* 3.8 44.5 + - + +
147S LEU* 1.3 78.2 - - - +
149S GLU* 1.3 77.8 + - - +
150S PRO 3.4 0.3 - - - -
----------------------------------------------------------
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