Contacts of the helix formed by residues 91 - 100 (chain K) 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 91 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A G 3.1 32.2 + - - +
616A U 4.1 21.0 + - - -
1105A C 4.3 13.3 + - - -
88K PRO* 3.0 25.4 + - + +
90K LYS* 1.3 83.4 - - - +
92K GLN* 1.3 66.1 + - - +
93K ARG* 4.3 14.0 - - + +
94K GLY 4.3 5.4 - - - +
95K ARG* 2.9 22.1 + - - +
8502K CL 3.8 6.9 - - + +
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Residues in contact with GLN 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A C 4.5 14.2 + - - -
614A U 4.0 34.9 + - - +
90K LYS 4.2 0.4 + - - -
91K LYS* 1.3 73.6 - - - +
93K ARG* 1.3 68.8 + - - +
95K ARG* 3.1 5.2 + - - +
96K GLU* 2.9 46.7 + - - +
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Residues in contact with ARG 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A G 5.0 4.6 + - - -
1104A C 4.8 1.8 + - - -
1105A C 3.4 26.3 + - - -
1106A A 5.6 1.6 + - - -
31K LEU* 4.3 35.0 + - + +
88K PRO* 4.2 17.2 - - - +
91K LYS* 3.4 17.7 - - + +
92K GLN* 1.3 82.9 + - - +
94K GLY* 1.3 55.7 + - - +
96K GLU* 3.2 14.9 + - - +
97K ALA* 3.0 27.7 + - - +
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Residues in contact with GLY 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LEU* 4.5 6.7 - - - -
87K LEU* 4.2 3.7 - - - +
88K PRO* 3.2 37.1 + - - -
89K HIS* 3.9 4.9 - - - -
91K LYS* 3.3 3.8 + - - +
92K GLN 3.2 0.8 - - - -
93K ARG* 1.3 79.3 - - - +
95K ARG* 1.3 58.5 + - - +
97K ALA* 3.3 2.1 + - - +
98K PHE* 3.0 29.8 + - - +
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Residues in contact with ARG 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A U 2.7 59.8 + - - +
534A C 4.1 11.3 + - - -
2814A A 3.0 33.3 + - - -
89K HIS* 3.6 19.6 - - - +
90K LYS 5.4 0.7 - - - -
91K LYS 2.9 18.4 + - - +
92K GLN* 3.7 5.4 - - - +
94K GLY* 1.3 72.8 - - - +
96K GLU* 1.3 65.5 + - - +
98K PHE* 3.9 9.3 - - + +
99K GLU* 2.7 48.8 + - + +
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Residues in contact with GLU 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K GLN* 2.9 40.5 + - + +
93K ARG* 3.3 14.4 - - - +
95K ARG* 1.3 78.7 - - - +
97K ALA* 1.3 62.8 + - - +
99K GLU* 3.3 7.3 + - - +
100K SER* 3.1 22.2 + - - -
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Residues in contact with ALA 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ALA* 3.3 36.2 - - + +
31K LEU* 3.7 23.3 - - + -
87K LEU* 4.3 4.5 - - + -
93K ARG 3.0 7.7 + - - +
94K GLY 3.3 7.2 + - - +
96K GLU* 1.3 77.2 - - - +
98K PHE* 1.3 64.3 + - - +
100K SER* 2.7 25.1 + - - -
101K VAL* 3.4 11.4 - - - +
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Residues in contact with PHE 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2815A G 5.4 4.7 - - - -
80K LYS* 3.3 51.9 - - + -
81K ARG* 5.6 0.4 - - - -
83K ILE* 4.6 6.3 - - + -
84K ARG* 3.5 52.9 - - + -
87K LEU* 3.6 16.7 - - + +
89K HIS* 4.8 7.9 - - + -
94K GLY 3.0 17.9 + - - +
95K ARG* 3.9 9.4 - - + +
97K ALA* 1.3 76.1 - - - +
99K GLU* 1.3 66.6 + - + +
101K VAL* 3.1 31.0 + - + +
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Residues in contact with GLU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2814A A 3.0 16.2 + - - -
2815A G 3.1 36.6 + - - +
6K PHE* 4.4 9.5 - - - -
80K LYS* 5.3 2.4 + - - +
95K ARG* 2.7 56.5 + - + +
96K GLU* 3.8 6.5 - - - +
97K ALA 3.1 0.2 - - - -
98K PHE* 1.3 79.7 - - + +
100K SER* 1.3 56.5 + - - +
101K VAL 3.1 10.7 + - - +
102K ARG* 4.7 6.4 + - - +
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Residues in contact with SER 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K PHE* 3.8 10.5 - - - -
30K ALA 4.4 2.4 + - - -
33K GLY 5.6 1.9 + - - -
34K GLU 3.9 11.6 + - - -
35K THR* 3.4 21.8 - - - +
36K VAL 3.0 23.9 + - - +
96K GLU 3.1 12.5 + - - -
97K ALA* 2.7 23.3 + - - -
99K GLU* 1.3 77.1 - - - +
101K VAL* 1.3 57.5 + - - +
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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