Contacts of the strand formed by residues 126 - 134 (chain N) 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 HIS 126 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32N ARG* 4.0 27.2 + - + +
66N ALA* 4.0 20.4 - - + -
67N ILE 3.4 10.1 - - - +
68N ARG* 4.7 0.4 - - - +
69N LYS* 3.1 11.7 - - - +
122N GLU* 3.1 19.9 - - - +
123N ASP* 2.7 33.8 + - - +
125N ARG* 1.3 95.0 - - + +
127N LYS* 1.3 63.6 + - - +
128N TRP* 3.5 32.4 - + + -
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Residues in contact with LYS 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A U 4.8 6.5 + - - -
403A C 2.8 39.4 + - - -
404A G 5.4 1.1 - - - -
65N VAL 3.5 2.3 - - - +
66N ALA* 3.6 1.0 - - - -
67N ILE* 2.9 36.0 + - - +
69N LYS* 3.7 8.7 - - + +
97N ILE* 3.6 35.8 - - + +
121N GLY 3.8 5.2 - - - +
122N GLU* 3.1 30.5 - - + +
126N HIS* 1.3 77.0 - - - +
128N TRP* 1.3 64.0 + - - +
129N HIS* 4.3 13.9 + - + -
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Residues in contact with TRP 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N MET* 3.7 20.2 - - + -
31N TRP* 3.6 39.3 + + + +
32N ARG* 3.9 21.8 - - + -
64N ARG* 4.0 18.4 - - + -
65N VAL 3.3 4.9 - - - +
66N ALA* 3.4 30.4 - - + +
119N SER* 3.7 2.3 + - - -
120N VAL* 2.9 40.2 + - + -
121N GLY 2.9 26.7 + - - +
122N GLU* 3.7 4.3 - - - -
123N ASP* 3.2 44.2 - - + -
126N HIS* 3.5 28.2 - + + -
127N LYS* 1.3 73.1 - - - +
129N HIS* 1.3 67.7 + - - +
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Residues in contact with HIS 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N VAL 3.5 0.7 - - - +
65N VAL* 2.8 32.7 + - - +
97N ILE* 4.0 14.0 - - + +
98N GLN* 3.5 49.4 + - + +
101N ALA* 4.1 21.3 - - + +
117N SER* 5.1 2.7 - - - +
118N TYR 3.1 8.7 - - - +
119N SER* 3.5 33.0 - - - -
120N VAL* 4.1 2.5 - - - -
127N LYS* 4.3 18.7 + - + -
128N TRP* 1.3 82.3 + - - +
130N GLU* 1.3 65.8 + - - +
131N VAL* 3.8 4.2 + - + +
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Residues in contact with GLU 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N ILE* 3.3 27.3 - - + +
43N PRO* 3.6 0.5 - - - +
44N THR* 2.6 48.5 + - - -
62N VAL* 4.3 4.3 - - + -
63N VAL 3.2 8.1 - - - +
64N ARG* 3.3 26.3 + - + -
117N SER* 3.3 3.3 - - - -
118N TYR* 2.6 67.5 + - + +
120N VAL* 3.5 14.0 - - + +
129N HIS* 1.3 72.7 - - - +
131N VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N VAL* 3.3 4.5 - - - -
63N VAL 2.7 37.2 + - - +
65N VAL* 4.4 6.3 - - + -
101N ALA* 4.2 5.8 - - + +
102N GLU* 4.0 15.5 - - - +
105N ALA* 3.9 28.0 - - + -
114N VAL* 3.8 24.2 - - + -
116N ASN 3.7 10.8 - - - +
117N SER* 3.9 12.1 - - - -
129N HIS* 4.4 4.9 - - + +
130N GLU* 1.3 76.2 - - - +
132N ILE* 1.3 63.5 + - - +
133N LEU* 3.3 20.5 - - + +
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Residues in contact with ILE 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N ALA* 3.9 23.1 - - + +
52N LEU* 3.9 37.7 - - + -
54N TYR* 4.1 16.8 - - + +
60N ILE* 4.4 11.0 - - + -
61N ILE 3.4 8.7 - - - +
62N VAL* 4.7 10.1 - - + -
114N VAL* 3.7 2.8 - - - -
115N LEU* 2.7 45.0 + - + -
116N ASN* 2.9 18.7 + - + +
118N TYR* 4.4 12.6 - - + -
131N VAL* 1.3 75.6 - - - +
133N LEU* 1.3 61.3 + - - +
134N ILE* 4.4 8.1 - - + -
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Residues in contact with LEU 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N ILE* 4.3 0.3 - - - +
61N ILE* 2.6 39.1 + - + +
63N VAL* 3.9 23.8 - - + -
105N ALA* 4.5 2.2 - - + -
106N ASN* 3.9 26.7 - - + +
109N PHE* 3.8 29.2 - - + -
112N LEU* 3.8 21.1 - - + -
113N ARG 3.3 8.7 - - - +
114N VAL* 4.5 8.1 - - + -
131N VAL* 3.3 33.0 - - + +
132N ILE* 1.3 76.7 - - - +
134N ILE* 1.3 72.1 + - - +
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Residues in contact with ILE 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N GLY 5.6 1.6 - - - +
59N GLY 3.4 1.8 - - - -
60N ILE* 3.7 30.5 - - + -
112N LEU* 3.4 6.3 - - - -
113N ARG* 2.9 24.3 + - - +
115N LEU* 3.7 31.9 - - + -
132N ILE* 4.4 4.3 - - + -
133N LEU* 1.3 86.3 - - - +
135N ASP* 1.3 63.7 + - - +
136N PRO* 2.9 14.9 - - - +
141N ILE* 3.4 33.7 - - + -
147N LEU* 4.7 12.8 - - + -
150N ILE* 3.9 25.6 - - + -
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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