Contacts of the strand formed by residues 94 - 98 (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 ALA 94 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18L ILE* 4.4 4.4 - - - +
19L THR* 3.2 11.7 - - - +
21L ALA* 4.0 6.5 - - + -
73L VAL* 3.7 3.3 - - - +
74L VAL* 2.8 31.1 + - + -
75L ARG* 2.7 60.5 + - - +
92L ASP* 4.1 3.1 - - - +
93L ASN* 1.3 77.2 - - - +
95L ALA* 1.3 57.7 + - - +
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Residues in contact with ALA 95 (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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18L ILE* 3.5 23.1 - - + +
19L THR 2.8 6.1 + - - -
20L CYS* 3.3 9.2 - - - -
21L ALA 2.9 21.9 + - - -
29L LEU* 4.1 12.7 - - + +
53L ILE* 4.7 4.3 - - + -
71L ALA* 4.3 8.7 - - + -
72L VAL 3.0 20.2 - - - +
73L VAL* 4.1 2.7 - - - -
74L VAL 4.1 1.1 - - - +
94L ALA* 1.3 75.6 - - - +
96L VAL* 1.3 65.6 + - - +
97L ILE 4.2 0.2 - - - -
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Residues in contact with VAL 96 (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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21L ALA* 3.5 25.6 - - + +
22L ASP* 3.7 10.5 - - + +
71L ALA* 3.8 2.9 - - - -
72L VAL* 2.9 29.0 + - + +
74L VAL* 3.7 23.3 - - + -
95L ALA* 1.3 77.6 - - - +
97L ILE* 1.3 75.8 + - - +
98L VAL* 3.3 4.0 + - - +
104L PRO* 4.2 11.7 - - + -
106L GLY 6.0 0.2 - - - +
109L LEU* 3.5 34.3 - - + -
113L ILE* 4.9 1.1 - - + -
124L VAL* 4.9 10.3 - - + -
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Residues in contact with ILE 97 (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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20L CYS* 3.8 10.8 - - - -
22L ASP* 3.1 10.6 + - - +
24L THR* 3.4 23.1 - - + +
26L ALA* 3.8 13.9 - - + -
29L LEU* 4.3 16.2 - - + -
55L VAL* 6.5 0.2 - - + -
64L MET* 3.8 17.9 - - + -
69L LEU* 3.9 25.4 - - + -
70L GLU 3.4 13.9 - - - +
71L ALA* 3.9 3.1 - - + +
95L ALA 4.2 0.4 + - - -
96L VAL* 1.3 76.5 - - - +
98L VAL* 1.3 68.0 + - - +
104L PRO* 3.5 6.6 - - - +
105L ARG* 3.0 43.4 + - + -
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Residues in contact with VAL 98 (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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52L LYS* 4.7 11.7 - - + -
69L LEU* 5.3 0.3 - - - +
70L GLU* 2.8 41.2 + - + +
71L ALA* 4.4 4.5 - - - +
72L VAL* 4.6 9.4 - - + -
96L VAL* 3.3 7.6 + - + +
97L ILE* 1.3 80.6 - - - +
99L ASP* 1.3 73.2 + - - +
102L GLU* 3.2 41.5 - - + +
103L ASP 3.6 9.9 - - - +
104L PRO* 4.0 2.5 - - + -
105L ARG* 4.3 3.8 - - - +
124L VAL* 4.1 13.9 - - + -
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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