Contacts of the helix formed by residues 77 - 95 (chain O) 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 ASN 77 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3049B G 3.4 15.9 - - - +
3050B G 3.0 36.1 + - - +
43O VAL* 5.3 0.5 - - - +
71O TRP* 4.7 4.1 - - - -
73O ALA* 5.5 0.6 - - - +
74O PRO* 3.6 24.8 + - - +
75O THR 3.5 1.6 - - - -
76O GLY* 1.3 76.1 - - - +
78O MET* 1.3 66.2 + - - +
79O PRO* 3.4 13.2 - - + +
80O SER* 2.9 32.9 + - - -
81O ALA* 3.0 22.0 + - - +
114O LYS* 3.9 7.4 - - - +
146O HIS* 5.6 0.4 - - + +
147O ILE* 4.9 2.6 - - + +
159O TYR* 4.1 5.1 + - - -
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Residues in contact with MET 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3048B C 4.0 9.0 - - - +
3049B G 2.9 23.7 + - - +
77O ASN* 1.3 73.3 - - - +
79O PRO* 1.3 69.9 - - + +
81O ALA* 3.1 4.3 + - - +
82O TYR* 3.0 22.5 + - - +
112O GLY 3.1 28.7 - - - +
113O SER 4.1 4.3 - - - +
114O LYS* 3.6 29.2 - - + -
117O ALA* 4.1 15.7 - - + +
137O ALA* 3.5 27.1 - - + +
141O ARG* 3.6 23.3 - - + +
142O THR* 3.8 9.1 - - - +
146O HIS* 3.9 9.2 - - + +
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Residues in contact with PRO 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O TRP* 4.4 12.3 - - + -
77O ASN* 3.4 17.7 - - + +
78O MET* 1.3 94.5 - - + +
80O SER* 1.3 60.7 + - - +
82O TYR* 3.6 0.6 + - + -
83O LEU* 3.0 33.6 + - - +
142O THR 3.0 23.3 - - - +
143O ARG 3.2 16.6 - - - +
144O GLY* 3.3 14.4 - - - -
146O HIS* 4.6 2.0 - - + -
147O ILE* 5.9 1.3 - - + -
172O PHE* 3.6 20.6 - - + -
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Residues in contact with SER 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O VAL* 5.0 1.3 - - - -
63O SER* 3.6 8.8 - - - -
66O LEU* 4.0 12.6 - - - +
71O TRP* 4.5 3.5 + - - -
74O PRO 4.2 2.0 + - - -
75O THR* 2.9 42.7 + - - +
77O ASN* 2.9 28.6 + - - -
79O PRO* 1.3 79.4 - - - +
81O ALA* 1.3 57.8 - - - +
83O LEU* 3.3 3.8 + - - +
84O THR* 2.9 32.6 + - - -
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Residues in contact with ALA 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O VAL* 3.7 20.7 - - + +
77O ASN 3.0 7.9 + - - +
78O MET 3.1 8.3 + - - +
80O SER* 1.3 75.0 - - - +
82O TYR* 1.3 67.5 + - - +
84O THR* 3.1 3.8 + - - -
85O GLY* 2.9 19.8 + - - -
114O LYS* 3.7 38.1 - - + +
117O ALA* 4.0 2.7 - - + -
118O ILE* 3.8 13.9 - - + +
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Residues in contact with TYR 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O MET 3.0 5.1 + - - +
79O PRO 3.8 6.3 - - - +
81O ALA* 1.3 77.6 - - - +
83O LEU* 1.3 66.5 + - + +
85O GLY* 2.8 5.9 + - - -
86O LEU* 2.8 46.6 + - + +
117O ALA* 3.7 17.6 - - + +
120O GLU* 4.1 11.0 - - + -
121O GLY* 3.6 23.6 - - - -
124O ASP* 2.7 28.3 + - + +
139O TRP* 3.9 12.1 - + - -
142O THR* 3.6 32.8 - - + -
172O PHE* 3.8 19.1 - + + -
176O ARG* 2.5 38.4 + - - -
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Residues in contact with LEU 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O LEU* 3.9 19.5 - - + -
71O TRP* 3.7 21.1 - - + -
79O PRO 3.0 19.0 + - - +
80O SER 3.6 3.1 - - - +
82O TYR* 1.3 83.8 - - + +
84O THR* 1.3 52.1 + - - +
86O LEU* 3.1 5.3 + - + +
87O LEU* 2.7 36.6 + - - +
172O PHE* 3.6 26.5 - - + -
175O LEU* 3.4 24.9 - - + -
176O ARG* 3.9 31.0 - - + +
179O LEU* 4.3 11.8 - - + +
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Residues in contact with THR 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O VAL* 3.2 26.9 - - + +
45O ALA* 4.2 6.1 - - + +
61O ALA* 3.1 39.0 - - + +
62O HIS 3.8 1.3 - - - +
63O SER* 3.3 26.7 - - - +
66O LEU* 4.3 6.8 - - - +
80O SER 2.9 15.4 + - - -
81O ALA 3.6 6.7 - - - -
83O LEU* 1.3 75.0 - - - +
85O GLY* 1.3 57.2 + - - +
87O LEU* 4.3 6.1 - - - -
88O ALA* 3.0 26.0 + - - +
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Residues in contact with GLY 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O LEU* 5.8 0.4 - - - +
45O ALA* 4.5 3.1 - - - -
81O ALA 2.9 8.9 + - - -
82O TYR 2.8 8.2 + - - -
84O THR* 1.3 78.1 - - - +
86O LEU* 1.3 50.8 + - - +
88O ALA* 3.3 2.3 + - - +
89O GLY* 2.7 33.1 + - - -
118O ILE* 3.5 31.1 - - - +
122O ALA* 3.5 14.2 - - - +
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Residues in contact with LEU 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O TYR* 2.8 30.2 + - + +
83O LEU* 3.5 7.2 - - + +
85O GLY* 1.3 76.3 - - - +
87O LEU* 1.3 56.6 + - - +
90O LEU* 2.8 50.0 + - + +
121O GLY* 3.5 15.9 - - - +
124O ASP* 4.1 4.9 - - + -
125O ALA* 3.4 35.6 - - + +
176O ARG* 4.4 13.5 - - + +
179O LEU* 4.0 26.9 - - + -
180O LEU* 4.1 20.6 - - + -
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Residues in contact with LEU 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O ALA* 3.8 5.4 - - + -
62O HIS 4.8 1.8 - - - +
65O ASP* 3.7 30.7 - - - +
66O LEU* 4.0 20.6 - - + -
69O TYR* 4.2 12.3 - - + -
83O LEU 2.7 20.7 + - - +
84O THR* 3.8 5.4 - - - +
86O LEU* 1.3 74.4 - - - +
88O ALA* 1.3 62.7 + - - +
90O LEU* 3.3 6.0 + - - -
91O ARG* 3.1 52.1 + - - +
179O LEU* 4.3 11.2 - - + +
186O LEU* 3.3 40.0 - - + +
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Residues in contact with ALA 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O LEU* 5.4 5.8 - - + -
45O ALA* 3.5 27.4 - - + +
46O GLN* 5.4 0.4 - - - -
47O LEU* 5.3 2.6 - - + +
59O ALA* 4.2 4.7 - - - +
60O SER* 4.0 9.2 - - - +
61O ALA* 3.2 24.1 - - + +
84O THR 3.0 12.5 + - - +
85O GLY 3.7 3.1 - - - +
87O LEU* 1.3 73.4 - - - +
89O GLY* 1.3 61.6 + - - +
91O ARG* 3.3 3.7 + - - +
92O ALA* 2.8 30.5 + - - +
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Residues in contact with GLY 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O LEU* 6.0 0.8 - - - +
85O GLY 2.7 20.8 + - - -
86O LEU 3.2 0.4 + - - -
88O ALA* 1.3 72.7 - - - +
90O LEU* 1.3 55.5 + - - +
92O ALA* 2.9 9.9 - - - +
93O GLN* 2.8 31.0 + - - +
122O ALA* 4.3 4.4 - - - +
125O ALA* 3.4 21.1 - - - -
127O LEU* 4.1 14.9 - - - +
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Residues in contact with LEU 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O LEU* 2.8 43.5 + - + +
87O LEU* 4.4 0.9 - - - -
88O ALA 3.3 0.2 - - - -
89O GLY* 1.3 72.6 - - - +
91O ARG* 1.3 67.5 + - - +
93O GLN* 2.9 9.8 + - + +
94O GLU* 2.9 22.7 + - - +
125O ALA* 3.4 28.5 - - + +
179O LEU* 3.3 30.3 - - + +
180O LEU* 5.1 6.1 - - + -
186O LEU* 3.4 36.3 - - + +
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Residues in contact with ARG 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O ALA* 3.9 12.3 - - + +
60O SER 3.0 27.9 + - - +
61O ALA* 3.5 10.1 - - - +
65O ASP* 3.0 28.9 + - - -
68O GLU* 4.7 1.0 + - - -
69O TYR* 3.4 23.6 + - - -
87O LEU* 3.1 32.4 + - - +
88O ALA 3.7 3.6 - - - +
90O LEU* 1.3 77.5 - - - +
92O ALA* 1.3 64.2 + - - +
94O GLU* 3.0 11.8 + - - +
95O ALA* 2.9 22.3 + - - +
185O GLU* 3.2 42.1 + - - +
186O LEU* 3.5 4.9 - - + +
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Residues in contact with ALA 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O LEU* 3.3 33.4 - - + -
59O ALA* 3.5 12.8 - - + +
88O ALA 2.8 14.6 + - - +
89O GLY 2.9 15.0 - - - +
91O ARG* 1.3 77.6 - - - +
93O GLN* 1.3 60.0 + - - +
95O ALA* 2.9 13.9 + - - +
97O VAL* 3.1 21.5 + - + +
127O LEU* 3.7 9.0 - - + -
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Residues in contact with GLN 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89O GLY 2.8 16.7 + - - +
90O LEU* 2.9 10.1 + - + +
92O ALA* 1.3 75.1 - - - +
94O GLU* 1.3 64.7 + - + +
96O GLY* 2.9 15.8 + - - -
97O VAL 2.7 29.1 + - - -
98O GLU* 3.9 12.0 + - - +
125O ALA 3.7 19.3 - - - +
126O GLY* 4.1 20.4 + - - +
127O LEU* 3.4 14.3 - - + +
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Residues in contact with GLU 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O LEU 2.9 9.8 + - - +
91O ARG* 3.3 11.9 - - - +
93O GLN* 1.3 77.4 - - - +
95O ALA* 1.3 58.7 + - - +
96O GLY* 3.2 4.7 + - - -
186O LEU* 2.9 39.1 - - - +
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Residues in contact with ALA 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O LEU* 3.8 27.7 - - + +
91O ARG 2.9 11.6 + - - +
92O ALA* 2.9 12.7 + - - +
94O GLU* 1.3 74.5 - - - +
96O GLY* 1.3 59.4 + - - +
97O VAL* 4.2 10.8 - - + +
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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
------------------------------------------------------------
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