Contacts of the helix formed by residues 74 - 85 (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 ARG 74 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2675A A 4.1 31.9 + - - +
2676A C 3.0 23.3 + - - +
91D PRO 3.0 25.9 + - - -
92D TYR* 3.7 20.2 - - - +
73K LYS* 1.3 78.7 - - - +
75K PRO* 1.3 70.2 - - + +
76K ASP* 2.8 42.0 + - + +
77K GLY 3.2 3.3 + - - +
78K ILE* 2.9 22.9 + - - +
105K LEU* 3.7 9.9 - - - +
136K SER* 3.4 1.6 - - - -
141K ALA* 4.5 9.4 - - + +
142K ASN* 4.6 8.2 + - - +
144K THR* 3.9 14.3 - - - +
145K TRP* 4.5 9.6 - - - -
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Residues in contact with PRO 75 (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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41K ALA* 3.9 6.7 - - - +
42K GLU* 3.8 31.2 - - + +
74K ARG* 1.3 82.7 - - + +
76K ASP* 1.3 62.3 + - - +
78K ILE* 4.1 8.1 - - + -
79K PHE* 3.4 21.1 + - - +
105K LEU* 3.3 23.6 - - + -
132K LEU* 3.8 21.0 - - + +
136K SER* 2.9 26.1 - - - +
145K TRP* 3.6 19.7 - - + -
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Residues in contact with ASP 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2815A G 4.7 4.7 + - - +
92D TYR* 3.9 16.4 + - - -
41K ALA* 4.8 3.4 - - - -
74K ARG* 2.8 39.7 + - + +
75K PRO* 1.3 85.7 - - - +
77K GLY* 1.3 63.1 + - - +
79K PHE* 3.5 3.5 + - - +
80K LYS* 3.3 13.8 + - - +
103K VAL* 3.2 37.5 - - - +
104K TYR* 4.1 4.7 - - - -
105K LEU* 3.8 17.9 + - + +
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Residues in contact with GLY 77 (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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72K PRO* 3.6 20.9 - - - -
74K ARG* 3.2 4.9 + - - +
76K ASP* 1.3 76.5 - - - +
78K ILE* 1.3 67.9 + - - +
79K PHE 3.0 2.5 - - - -
80K LYS* 2.6 9.4 + - - -
81K ARG* 2.6 24.9 + - - +
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Residues in contact with ILE 78 (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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1242A A 4.8 0.7 + - - -
19K MET* 3.4 19.7 - - + -
57K TYR* 3.8 28.3 - - + -
71K TYR* 3.5 20.0 + - + +
72K PRO* 2.9 36.6 - - - +
73K LYS* 4.1 7.4 - - - +
74K ARG 2.9 28.3 + - - +
75K PRO* 4.0 8.5 - - + +
77K GLY* 1.3 72.0 - - - +
79K PHE* 1.3 57.2 + - - +
81K ARG* 3.4 2.7 + - - +
82K THR* 2.6 34.4 + - - +
132K LEU* 4.4 8.5 - - + +
135K ILE* 5.4 4.7 - - + -
136K SER* 4.5 2.5 - - - +
139K LEU* 4.3 6.7 - - + -
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Residues in contact with PHE 79 (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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14K ALA* 3.8 13.2 - - + -
19K MET* 3.4 35.0 - - + -
22K VAL* 3.9 30.5 - - + -
23K ALA* 4.2 7.4 - - + -
38K VAL* 3.9 11.0 - - + -
41K ALA* 4.2 10.8 - - + -
44K ALA* 3.8 21.5 - - + -
75K PRO 3.4 14.4 + - - +
76K ASP 3.7 3.6 - - - +
77K GLY 3.0 0.6 - - - -
78K ILE* 1.3 79.6 - - - +
80K LYS* 1.3 64.8 + - - +
82K THR* 3.2 2.4 + - - -
83K ILE* 3.1 41.1 + - + +
103K VAL* 3.8 11.4 - - + -
132K LEU* 3.9 16.6 - - + -
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Residues in contact with LYS 80 (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 2.6 56.0 + - + +
76K ASP 3.3 7.5 + - - +
77K GLY* 2.6 17.6 + - - +
79K PHE* 1.3 75.5 - - - +
81K ARG* 1.3 61.3 + - - +
83K ILE* 2.9 9.3 + - + +
84K ARG 2.9 19.6 + - - -
98K PHE* 3.3 43.3 + - + -
99K GLU* 5.3 2.6 + - - +
101K VAL* 3.0 27.8 + - + +
102K ARG* 4.2 0.2 - - - +
103K VAL* 3.9 17.7 - - + +
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Residues in contact with ARG 81 (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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1241A G 4.8 1.9 - - - +
1242A A 5.4 2.7 - - - +
2081A A 4.6 11.1 + - - -
2082A G 3.2 16.2 + - - -
69K TYR* 4.6 9.5 + - - -
70K PHE* 2.8 43.9 + - - -
71K TYR* 4.0 28.7 - - + +
72K PRO* 4.1 15.6 - - + +
77K GLY 2.6 18.0 + - - +
78K ILE 3.8 3.8 - - - +
80K LYS* 1.3 72.2 - - - +
82K THR* 1.3 63.5 + - - +
84K ARG* 3.2 49.6 + - - +
85K GLY* 3.1 19.9 + - - +
98K PHE* 5.6 0.7 - - - -
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Residues in contact with THR 82 (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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1241A G 2.6 24.8 + - - -
1242A A 3.1 50.3 + - - -
19K MET* 3.5 24.9 - - + +
20K GLY* 4.8 0.2 - - - -
23K ALA* 3.9 19.3 - - + -
78K ILE* 2.6 20.7 + - - +
79K PHE* 3.3 11.7 - - - -
80K LYS 3.1 0.2 - - - -
81K ARG* 1.3 78.0 - - - +
83K ILE* 1.3 63.5 + - - +
85K GLY 3.3 1.2 + - - -
86K MET* 3.8 6.4 + - + +
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Residues in contact with ILE 83 (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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23K ALA* 3.8 23.6 - - + +
26K VAL* 4.2 15.0 - - + -
27K ALA* 4.7 15.9 - - + -
38K VAL* 4.4 3.4 - - + -
79K PHE* 3.3 31.2 - - + +
80K LYS* 2.9 9.4 + - + +
82K THR* 1.3 71.8 - - - +
84K ARG* 1.3 56.9 + - - +
85K GLY 3.0 2.2 - - - -
86K MET* 2.7 32.2 + - - +
87K LEU* 3.5 21.8 + - + +
98K PHE* 4.6 5.8 - - + -
101K VAL* 4.1 30.7 - - + -
103K VAL* 4.3 11.4 - - + -
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Residues in contact with ARG 84 (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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2081A A 2.7 31.9 + - - -
2082A G 3.0 28.6 + - - -
80K LYS 2.9 8.0 + - - +
81K ARG* 3.2 48.3 + - - +
83K ILE* 1.3 76.6 - - - +
85K GLY* 1.3 58.0 + - - +
87K LEU* 3.0 28.5 + - - +
89K HIS* 3.6 43.4 + - + -
98K PHE* 3.5 39.9 - - + -
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Residues in contact with GLY 85 (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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1104A C 4.8 1.7 + - - -
1240A G 2.9 24.2 + - - +
1241A G 3.3 30.0 - - - +
2081A A 5.7 4.9 - - - -
81K ARG* 3.1 12.2 + - - -
82K THR 3.3 0.2 + - - -
83K ILE 3.0 1.8 - - - -
84K ARG* 1.3 75.5 - - - +
86K MET* 1.3 56.3 + - - +
87K LEU 3.3 3.8 + - - +
89K HIS* 5.6 1.3 - - - -
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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