Contacts of the strand formed by residues 52 - 60 (chain L) 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 LYS 52 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1L MET* 4.9 11.1 - - + +
34L VAL* 3.8 1.4 - - - +
35L HIS* 2.8 70.1 + - + +
50L GLY 4.0 1.4 + - - -
51L ASP* 1.3 71.9 - - - +
53L ILE* 1.3 61.6 + - - +
70L GLU* 4.0 32.4 + - + +
71L ALA 3.3 15.3 - - - +
72L VAL* 4.5 10.5 - - + +
98L VAL* 4.7 11.9 - - + -
99L ASP 5.8 0.2 + - - -
100L GLU 5.2 3.8 + - - -
102L GLU* 3.0 32.5 + - + +
121L PHE* 4.6 8.2 - - + -
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Residues in contact with ILE 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L LEU* 5.4 0.4 - - + -
18L ILE* 4.3 10.5 - - + -
31L VAL* 3.9 23.6 - - + -
33L SER 3.1 14.4 - - - +
34L VAL* 4.4 2.5 - - - -
35L HIS* 4.3 0.9 - - - +
47L ALA* 3.8 28.0 - - + -
51L ASP* 4.0 5.8 - - + +
52L LYS* 1.3 78.4 - - - +
54L THR* 1.3 61.3 + - - +
55L VAL* 3.3 24.9 - - + -
70L GLU* 3.7 5.7 - - - +
71L ALA 2.9 37.1 + - - +
73L VAL* 3.9 27.8 - - + -
95L ALA* 4.7 3.8 - - + -
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Residues in contact with THR 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2596A A 3.8 32.1 - - - +
2597A U 3.1 26.0 + - - +
31L VAL* 3.9 1.0 - - - -
32L ILE* 2.9 27.4 + - + -
33L SER* 2.8 16.2 + - - +
35L HIS* 5.1 2.1 + - - +
53L ILE* 1.3 70.3 - - - +
55L VAL* 1.3 72.8 + - - +
68L VAL* 3.9 19.1 - - + -
69L LEU 3.7 10.8 - - - +
70L GLU* 4.6 10.1 + - + +
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Residues in contact with VAL 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 3.2 40.6 - - + -
30L LYS 3.0 20.6 - - - +
31L VAL* 4.5 1.1 - - + -
32L ILE* 4.0 5.6 - - - +
53L ILE* 3.3 35.2 - - + +
54L THR* 1.3 84.0 - - - +
56L SER* 1.3 72.7 + - - +
57L VAL* 6.0 0.4 - - - -
68L VAL* 3.2 7.1 - - - +
69L LEU* 2.7 43.0 + - + +
71L ALA* 4.1 14.6 - - + -
97L ILE* 6.5 0.2 - - + -
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Residues in contact with SER 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1993A C 2.7 39.0 + - - -
29L LEU* 3.6 0.7 - - - -
30L LYS* 2.9 38.9 + - - +
32L ILE* 3.5 18.2 - - - -
55L VAL* 1.3 82.2 - - - +
57L VAL* 1.3 64.7 + - - +
58L THR* 3.4 0.7 + - - -
66L ARG 5.2 0.7 - - - -
67L GLN 3.2 8.5 - - - -
68L VAL* 4.4 2.2 - - - -
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Residues in contact with VAL 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1993A C 5.0 3.2 + - - -
26L ALA* 3.9 21.5 - - + -
28L GLU 3.8 4.5 - - - +
29L LEU* 3.7 18.8 - - + -
55L VAL 5.9 0.4 - - - +
56L SER* 1.3 72.0 + - - +
58L THR* 1.3 63.1 + - - +
59L LYS 3.2 29.6 - - - +
64L MET* 3.2 29.4 - - + +
65L ARG* 3.8 7.9 - - - +
66L ARG* 3.0 26.6 + - - +
67L GLN 3.0 12.7 + - - +
69L LEU* 4.2 17.7 - - + -
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Residues in contact with THR 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1993A C 5.0 1.2 + - - -
17L LEU* 4.0 7.1 - - + +
28L GLU* 2.8 44.9 + - - +
30L LYS* 3.6 34.3 + - - +
56L SER* 3.4 1.6 + - - -
57L VAL* 1.3 74.6 - - - +
59L LYS* 1.3 65.6 + - + +
65L ARG* 3.9 13.6 - - - +
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Residues in contact with LYS 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ARG* 2.8 30.7 + - + -
28L GLU* 3.2 48.6 + - + +
57L VAL* 3.2 13.9 - - - +
58L THR* 1.3 85.7 - - + +
60L GLY* 1.3 61.3 + - - +
65L ARG* 4.4 3.1 - - - +
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Residues in contact with GLY 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L GLY 3.2 12.3 - - - -
26L ALA* 4.4 0.7 - - - -
27L ARG* 4.0 18.7 - - - +
57L VAL* 4.9 1.1 - - - -
59L LYS* 1.3 76.5 - - - +
61L THR* 1.3 67.3 + - - -
62L PRO* 3.5 2.3 - - - +
65L ARG* 3.3 18.9 + - - +
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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