Contacts of the helix formed by residues 110 - 124 (chain Z) 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 110 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109Z LEU* 1.3 78.5 - - - +
111Z ASP* 1.3 64.9 + - - +
112Z GLU* 3.6 7.3 + - - +
113Z ASP* 3.0 32.2 + - - +
114Z ALA* 3.1 15.8 + - - +
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Residues in contact with ASP 111 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Z LEU 3.5 2.4 + - - +
110Z SER* 1.3 74.5 - - - +
112Z GLU* 1.3 62.8 + - - +
114Z ALA* 3.4 5.7 + - - +
115Z ARG* 3.1 22.2 + - - +
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Residues in contact with GLU 112 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267A C 3.9 10.4 + - - -
110Z SER* 3.1 7.0 + - - +
111Z ASP* 1.3 77.7 - - - +
113Z ASP* 1.3 69.6 + - - +
115Z ARG* 2.4 49.5 + - - +
116Z LEU* 3.0 41.4 + - + +
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Residues in contact with ASP 113 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Z LEU* 4.0 18.1 - - + +
110Z SER* 3.0 26.7 + - - +
112Z GLU* 1.3 81.5 - - - +
114Z ALA* 1.3 57.1 + - - +
116Z LEU* 3.2 5.3 + - - -
117Z LEU* 2.8 29.6 + - - +
173Z ALA* 3.7 23.2 - - - +
174Z VAL* 3.6 6.4 - - + +
177Z LYS* 3.3 25.7 + - - +
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Residues in contact with ALA 114 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Z LEU* 4.3 18.1 - - + +
110Z SER 3.1 14.5 + - - +
111Z ASP* 3.9 5.6 - - - +
113Z ASP* 1.3 77.5 - - - +
115Z ARG* 1.3 60.8 + - - +
117Z LEU* 3.9 8.7 - - + +
118Z THR* 3.0 29.8 + - - -
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Residues in contact with ARG 115 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A U 5.3 12.5 - - - +
1266A U 2.7 52.2 + - - -
1267A C 3.8 1.4 + - - -
8517A CL 3.5 30.1 - - + +
111Z ASP 3.1 14.0 + - - +
112Z GLU* 2.4 60.2 + - - +
113Z ASP 3.1 0.2 - - - -
114Z ALA* 1.3 79.7 - - - +
116Z LEU* 1.3 72.9 + - + +
118Z THR* 3.2 7.0 + - - +
119Z GLN* 2.9 27.1 + - + +
122Z ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 116 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266A U 4.3 2.5 - - - +
1267A C 3.7 33.2 - - - +
1268A C 5.9 0.4 - - - +
112Z GLU* 3.0 31.2 + - + +
113Z ASP 3.7 3.6 - - - +
115Z ARG* 1.3 97.4 - - - +
117Z LEU* 1.3 64.6 + - - +
119Z GLN* 3.2 10.8 + - - +
120Z ARG* 3.0 23.6 + - - +
171Z PRO* 4.2 20.4 - - + +
173Z ALA* 3.8 25.1 - - + -
174Z VAL* 3.8 12.7 - - + +
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Residues in contact with LEU 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Z LEU* 4.4 10.8 - - + -
113Z ASP 2.8 19.7 + - - +
114Z ALA* 3.9 7.6 - - + +
115Z ARG 3.3 0.2 - - - -
116Z LEU* 1.3 73.3 - - - +
118Z THR* 1.3 63.0 + - - +
120Z ARG* 3.4 22.5 + - - +
121Z HIS* 3.1 24.0 + - + +
174Z VAL* 3.2 31.8 - - + +
177Z LYS* 4.3 11.9 - - + -
178Z HIS 4.4 4.5 - - - +
179Z PRO 3.8 14.4 - - - +
180Z SER 4.3 3.4 - - - +
181Z GLY* 3.8 22.7 - - - +
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Residues in contact with THR 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A U 3.6 41.5 - - - +
596A C 4.0 13.9 + - - +
114Z ALA* 3.0 20.1 + - - +
115Z ARG* 3.5 5.8 - - - +
117Z LEU* 1.3 77.4 - - - +
119Z GLN* 1.3 64.1 + - - +
121Z HIS* 3.5 8.7 + - - +
122Z ARG* 3.0 22.7 + - + +
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Residues in contact with GLN 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1265A G 5.6 1.4 - - - +
1266A U 2.7 39.7 + - - +
1267A C 3.2 27.6 + - - +
115Z ARG* 2.9 17.4 + - + +
116Z LEU* 3.2 15.6 + - - +
118Z THR* 1.3 73.6 - - - +
120Z ARG* 1.3 68.9 + - - +
122Z ARG* 2.9 28.5 + - - +
123Z VAL* 2.8 41.6 + - + +
171Z PRO* 3.9 10.4 - - + +
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Residues in contact with ARG 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326A U 3.9 16.9 + - - -
1327A G 2.9 39.6 + - - +
116Z LEU 3.0 12.5 + - - +
117Z LEU* 3.6 21.6 + - - +
119Z GLN* 1.3 75.6 - - - +
121Z HIS* 1.3 66.7 + - - +
123Z VAL* 5.0 2.2 - - - -
124Z GLY* 2.9 27.2 + - - +
170Z SER* 4.2 20.9 - - - -
171Z PRO* 4.4 10.9 - - + +
174Z VAL* 3.2 34.1 + - + +
177Z LYS 2.9 29.3 + - - +
178Z HIS 4.0 4.2 + - - -
179Z PRO* 4.0 6.7 - - - +
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Residues in contact with HIS 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A U 3.7 21.5 + - - -
556A C 3.3 28.8 + - - -
607A G 5.3 14.1 + - - -
117Z LEU* 3.1 15.2 + - + +
118Z THR* 3.8 8.9 + - - +
120Z ARG* 1.3 85.3 - - - +
122Z ARG* 1.3 64.8 + - - +
124Z GLY* 4.2 4.7 + - - -
179Z PRO* 6.2 3.8 - - + -
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Residues in contact with ARG 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A C 3.1 47.2 + - - -
595A U 3.1 27.3 + - - +
1091A U 5.3 3.9 + - - -
1265A G 5.5 7.1 - - - +
8517A CL 4.1 5.5 - - - +
115Z ARG 5.0 0.4 + - - -
118Z THR* 3.0 14.0 + - + +
119Z GLN* 2.9 44.6 + - - +
121Z HIS* 1.3 83.0 + - - +
123Z VAL* 1.3 75.4 + - - +
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Residues in contact with VAL 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A A 5.3 4.5 + - - -
1090A A 4.7 6.5 - - - +
1091A U 3.8 49.7 - - - +
119Z GLN* 2.8 39.4 + - + +
120Z ARG* 4.3 2.5 - - - +
122Z ARG* 1.3 87.3 - - - +
124Z GLY* 1.3 72.5 + - - +
125Z LYS* 3.8 0.5 + - - -
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Residues in contact with GLY 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A A 5.7 0.3 + - - -
120Z ARG* 2.9 20.8 + - - -
121Z HIS* 4.7 4.5 - - - -
122Z ARG 3.5 1.4 - - - -
123Z VAL* 1.3 86.4 - - - +
125Z LYS* 1.3 65.5 + - - +
168Z PHE 5.7 0.2 - - - +
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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