Contacts of the strand formed by residues 17 - 25 (chain F) 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 ARG 17 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3030B C 3.2 28.5 + - - -
3031B C 4.8 11.7 + - - -
15F GLU 4.7 1.8 - - - +
16F PRO* 1.3 78.4 - - - +
18F ILE* 1.3 70.4 + - - +
19F GLU* 3.6 18.4 + - - +
134F LEU* 3.7 7.9 - - - +
135F VAL* 3.1 37.1 + - + +
136F ARG 4.8 0.4 - - - -
137F PRO* 3.7 25.7 + - + +
139F TYR* 4.1 23.0 - - - +
140F ARG* 5.0 2.0 - - - +
165F PHE* 4.0 10.7 - - - -
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Residues in contact with ILE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ARG* 1.3 80.0 + - - +
19F GLU* 1.3 63.7 + - - +
20F LYS 4.0 6.3 + - - +
21F VAL* 3.9 24.0 - - + -
77F ASP* 5.1 8.4 + - - +
80F ALA* 4.3 10.8 - - + +
81F GLU* 5.3 14.8 - - + -
84F LEU* 3.2 30.7 - - + -
132F VAL* 4.2 6.5 - - + -
134F LEU* 3.4 21.5 - - + -
165F PHE* 4.2 14.6 - - + -
166F ILE* 6.1 2.2 - - + -
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Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3044B A 4.5 16.2 + - - +
17F ARG* 3.6 18.5 + - - +
18F ILE* 1.3 73.0 - - - +
20F LYS* 1.3 85.4 + - - +
76F ARG* 4.6 21.3 + - - +
133F ASN* 2.9 41.1 + - - +
135F VAL* 4.3 17.8 - - + +
139F TYR* 3.1 41.6 - - - -
143F LYS* 5.4 0.6 - - - -
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Residues in contact with LYS 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2348A C 2.8 20.6 + - - -
2349A G 2.6 26.9 + - - -
18F ILE* 3.9 4.5 + - - +
19F GLU* 1.3 96.7 - - - +
21F VAL* 1.3 65.2 + - - +
22F VAL* 4.4 16.1 + - + +
74F THR* 4.9 5.5 - - + +
75F LEU 2.8 19.4 + - - +
76F ARG* 3.6 53.0 - - - +
133F ASN* 3.2 42.2 + - + +
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Residues in contact with VAL 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ILE* 3.9 12.6 - - + -
20F LYS* 1.3 78.3 - - - +
22F VAL* 1.3 60.8 + - - +
23F VAL* 3.7 2.9 + - + -
73F VAL 3.1 4.5 - - - +
75F LEU* 2.9 35.2 + - + +
80F ALA* 3.7 26.0 - - + +
83F PHE* 4.4 13.5 - - + -
84F LEU* 3.9 17.9 - - + -
130F VAL* 3.7 25.6 - - + -
131F THR 3.0 19.1 - - - +
132F VAL* 4.1 7.9 - - + -
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Residues in contact with VAL 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2347A C 3.2 27.9 + - - +
2348A C 3.6 27.6 - - - -
20F LYS* 4.4 16.4 - - + +
21F VAL* 1.3 73.1 - - - +
23F VAL* 1.3 64.3 + - - +
24F HIS 3.8 1.0 + - - -
72F LYS* 4.1 23.3 - - + -
73F VAL 3.2 7.9 - - - +
74F THR* 3.8 20.0 - - + -
129F ASP* 3.6 1.7 - - - +
130F VAL* 3.5 1.7 - - - -
131F THR* 2.9 40.0 + - - +
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Residues in contact with VAL 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F VAL* 4.5 7.4 - - + +
22F VAL* 1.3 72.5 - - - +
24F HIS* 1.3 58.9 + - - +
41F LEU* 3.5 21.1 - - + +
44F ILE* 5.6 0.7 - - + -
45F THR* 3.3 27.4 - - + -
72F LYS* 3.2 2.4 - - - -
73F VAL* 2.8 40.6 + - + +
75F LEU* 4.7 1.6 - - + -
83F PHE* 3.4 41.5 - - + -
128F LEU* 5.6 1.6 - - + -
129F ASP 3.2 7.9 - - - +
130F VAL* 3.7 12.1 - - + -
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Residues in contact with HIS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2338A G 3.5 9.2 - - - -
2346A C 2.8 48.1 + - - -
2347A C 3.3 33.8 + - - +
22F VAL 3.8 1.6 + - - -
23F VAL* 1.3 75.6 - - - +
25F MET* 1.3 63.7 + - - +
26F GLY* 3.0 28.3 + - - -
41F LEU* 4.6 0.7 - - - -
52F THR* 4.3 2.5 - - + -
71F ALA 3.1 25.6 - - - +
72F LYS* 3.4 14.4 - - + -
128F LEU* 4.1 0.8 - - - +
129F ASP* 3.1 41.0 + - + +
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Residues in contact with MET 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F HIS* 1.3 76.7 - - - +
26F GLY* 1.3 60.4 + - - +
27F ILE* 2.8 25.1 + - + +
37F ALA* 2.9 50.3 - - + +
40F ILE* 3.4 23.1 - - + -
41F LEU* 3.2 30.7 - - + +
70F GLY* 3.4 13.5 - - - -
71F ALA* 3.0 10.4 + - + +
128F LEU* 4.1 33.4 - - + +
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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