Contacts of the strand formed by residues 110 - 122 (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 THR 110 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37S GLY* 4.0 21.1 - - - +
38S LYS 3.6 3.8 - - - -
39S THR* 4.5 4.8 + - - +
108S ALA 3.8 1.1 + - - -
109S MET* 1.3 72.5 - - - +
111S ILE* 1.3 74.0 + - - +
112S LYS* 2.9 9.8 + - + +
147S LEU* 3.2 4.8 - - - -
148S GLU* 2.8 47.5 + - - +
149S GLU 5.5 0.4 - - - -
150S PRO* 4.4 15.7 - - - +
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Residues in contact with ILE 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S ILE* 3.5 28.9 - - + +
36S LYS* 3.9 5.9 - - - +
37S GLY* 3.0 23.0 + - - +
38S LYS 2.8 20.4 + - - +
40S ALA* 4.3 5.2 - - - +
43S ALA* 3.7 27.4 - - + -
92S LEU* 4.1 10.1 - - + -
110S THR* 1.3 72.0 - - - +
112S LYS* 1.3 62.6 + - - +
113S HIS 4.0 1.3 - - - +
114S VAL* 3.9 22.9 - - + -
145S LEU* 3.4 24.0 - - + -
146S ILE 3.8 3.8 - - - -
147S LEU* 4.1 15.0 - - + -
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Residues in contact with LYS 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S VAL* 4.6 10.8 - - + +
7S GLU 3.4 23.9 + - - +
8S ALA* 4.7 4.6 - - - +
9S ASP 5.4 1.2 - - - +
13S THR* 5.0 2.1 + - - +
36S LYS* 3.5 19.6 + - - -
110S THR* 2.9 9.7 + - - -
111S ILE* 1.3 73.5 - - - +
113S HIS* 1.3 65.0 + - + +
146S ILE* 2.9 30.0 + - + +
148S GLU* 3.8 47.3 + - + +
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Residues in contact with HIS 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A G 3.4 26.0 + - - +
5S SER* 3.5 8.7 + - - -
6S VAL* 3.5 27.8 - - + +
36S LYS* 4.9 10.1 - - + +
111S ILE* 3.3 1.1 - - - -
112S LYS* 1.3 86.2 - - + +
114S VAL* 1.3 67.3 + - - +
115S ALA* 4.0 13.8 - - + +
144S GLU* 3.1 46.8 + - + +
145S LEU* 3.0 9.2 - - - +
146S ILE* 2.7 52.8 + - + +
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Residues in contact with VAL 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A G 4.7 8.7 - - - +
32S ALA* 3.7 34.7 - - + +
35S ILE* 4.4 8.5 - - + -
36S LYS* 3.5 39.9 - - + +
88S PHE* 4.1 16.4 - - + -
91S LEU* 5.2 1.1 - - + -
111S ILE* 3.9 4.3 - - + -
113S HIS* 1.3 81.7 - - - +
115S ALA* 1.3 68.6 + - - +
143S VAL* 4.4 2.5 - - + -
144S GLU 3.2 12.6 - - - +
145S LEU* 3.8 15.9 - - + -
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Residues in contact with ALA 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A A 3.5 17.0 - - - +
525A G 3.8 15.7 - - - +
32S ALA* 4.3 6.3 - - - -
113S HIS* 4.0 16.2 - - + +
114S VAL* 1.3 79.2 - - - +
116S ALA* 1.3 59.4 + - - +
117S HIS* 3.7 15.1 + - + -
143S VAL* 3.1 7.5 - - - +
144S GLU* 3.0 34.4 + - - +
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Residues in contact with ALA 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A A 2.8 32.8 + - - +
25S PHE* 3.6 10.4 - - + -
28S SER* 3.6 39.9 - - - +
29S LYS* 4.3 3.5 - - - +
32S ALA* 4.5 3.0 - - - +
88S PHE* 4.9 1.6 - - + -
115S ALA* 1.3 72.2 - - - +
117S HIS* 1.3 63.9 + - - +
141S VAL* 4.0 9.4 - - + -
142S ASP 3.5 4.7 - - - -
143S VAL* 4.1 8.1 - - + -
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Residues in contact with HIS 117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A G 3.2 35.1 + - - +
21A G 4.6 6.7 - - - +
523A C 5.7 1.3 - - - +
524A A 3.2 29.3 + - - -
2S ILE* 3.8 35.2 - - + +
5S SER* 4.8 1.2 + - - -
25S PHE* 3.6 6.3 - - - -
115S ALA* 3.7 25.2 + - + -
116S ALA* 1.3 75.1 - - - +
118S LYS* 1.3 63.5 + - - +
119S VAL* 3.2 2.3 + - + +
141S VAL* 3.6 1.4 - - - -
142S ASP 2.9 32.6 + - - +
144S GLU* 3.1 29.5 + - + -
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Residues in contact with LYS 118 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A G 4.0 16.4 + - - +
22A U 4.2 8.3 + - - +
523A C 5.1 3.7 + - - +
1366A C 4.7 17.4 + - - +
25S PHE* 3.3 37.0 - - + -
117S HIS* 1.3 68.2 - - - +
119S VAL* 1.3 61.8 + - - +
120S GLY* 4.0 13.9 - - - +
121S GLU* 3.5 39.3 + - - -
139S PRO* 4.1 14.4 - - - +
140S GLN 3.5 8.3 - - - +
8506S CL 3.3 29.1 - - + +
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Residues in contact with VAL 119 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A G 4.3 9.6 - - - +
22A U 3.4 41.7 - - - +
23A G 5.0 1.6 + - - -
1S GLY* 4.2 11.2 - - - +
2S ILE* 4.4 3.4 - - + -
20S GLU* 4.7 16.6 - - + +
117S HIS 3.6 4.7 - - - +
118S LYS* 1.3 73.4 - - - +
120S GLY* 1.3 56.1 + - - +
140S GLN* 2.8 17.0 + - + +
142S ASP* 3.1 47.1 - - + +
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Residues in contact with GLY 120 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A U 5.1 6.1 - - - -
23A G 5.5 2.7 - - - -
118S LYS* 3.4 10.4 + - - +
119S VAL* 1.3 82.0 - - - +
121S GLU* 1.3 65.6 + - - +
139S PRO* 3.6 1.0 - - - +
140S GLN* 2.7 41.8 + - - +
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Residues in contact with GLU 121 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366A C 6.0 1.6 - - - -
2054A A 4.9 5.2 + - - -
118S LYS* 3.5 28.2 + - - -
120S GLY* 1.3 79.7 - - - +
122S GLN* 1.3 59.8 + - - +
123S GLN* 3.0 21.1 + - + +
137S ASN* 3.2 40.4 + - + +
138S SER 3.1 10.9 - - - +
139S PRO* 4.6 2.5 - - + +
140S GLN* 3.6 7.2 + - - +
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Residues in contact with GLN 122 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427A A 4.1 1.4 + - - +
1428A C 2.9 39.1 + - - +
1429A U 3.7 24.2 + - - +
22S GLN* 3.0 25.7 + - - +
121S GLU* 1.3 69.0 - - - +
123S GLN* 1.3 67.5 + - - +
136S TRP 4.6 0.2 - - - +
137S ASN* 3.5 1.7 - - - -
138S SER* 2.7 47.6 + - - +
140S GLN* 3.9 20.1 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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