Contacts of the helix formed by residues 82 - 95 (chain A) in PDB entry 1N54
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A CYS 5.4 0.2 + - - -
39A GLY* 3.4 35.8 - - - -
40A GLU* 3.8 15.0 - - - +
79A LEU* 3.2 30.2 + - + +
80A PRO 2.8 1.4 + - - -
81A GLU* 1.3 96.2 - - + +
83A LEU* 1.3 68.0 + - - +
84A THR* 3.7 2.2 - - - -
85A ILE* 3.1 23.0 + - + +
86A TYR* 3.2 38.9 + - + +
335A GLN* 4.2 19.1 + - - +
340A PRO* 5.6 11.7 - - + -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ALA 5.2 2.2 - - - +
79A LEU 3.5 3.8 + - - -
80A PRO* 2.6 30.5 + - + +
81A GLU 3.4 1.2 + - - -
82A LYS* 1.3 73.3 - - - +
84A THR* 1.3 69.7 + - + +
85A ILE 2.8 0.3 + - - -
86A TYR* 2.9 11.5 + - - +
87A THR* 3.1 14.0 + - + +
126A TYR 4.5 4.9 - - - +
129A ARG* 4.2 19.7 - - + +
130A PHE* 3.5 49.0 - - + +
133A ASP* 4.9 2.2 - - + -
179A TRP* 3.6 47.8 - - + +
317A ASN* 6.0 0.2 - - - +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS 4.9 0.7 + - - -
83A LEU* 1.3 79.3 + - + +
85A ILE* 1.3 64.6 + - - +
87A THR* 2.6 23.3 + - - -
88A THR* 3.1 15.1 + - - -
133A ASP* 3.7 17.0 - - - +
179A TRP* 3.8 13.0 - - + +
249A ILE* 3.4 25.5 - - + +
250A LEU* 2.7 33.3 + - - +
251A ARG* 4.9 0.9 - - - -
252A PRO* 3.5 8.4 - - - +
253A TYR* 4.5 3.8 - - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.5 4.9 - - + -
39A GLY* 3.9 26.9 - - - +
46A LEU* 3.6 47.1 - - + -
50A LEU* 3.3 17.5 - - + +
82A LYS* 3.1 21.0 + - + +
83A LEU 2.8 5.7 + - - -
84A THR* 1.3 79.3 + - - +
86A TYR* 1.3 70.7 + - + +
88A THR* 3.5 2.1 + - - -
89A LEU 3.3 17.7 + - - -
250A LEU* 6.4 2.5 - - + -
252A PRO* 3.6 9.6 - - + -
340A PRO* 6.1 4.9 - - + -
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.0 39.5 + - + -
36A CYS* 3.2 20.6 + - - -
38A VAL* 3.9 9.6 - - + -
39A GLY* 3.3 7.0 + - - -
50A LEU* 6.5 0.2 - - + -
72A LEU* 4.4 12.6 - - + +
75A VAL* 3.3 42.4 - - + +
79A LEU* 4.9 5.6 - - + +
82A LYS* 3.2 43.2 + - + +
83A LEU* 2.9 6.2 + - - +
85A ILE* 1.3 80.7 - - + +
87A THR* 1.3 66.6 + - - +
88A THR 3.1 1.3 - - - -
89A LEU* 3.4 11.4 + - + +
90A VAL* 2.9 28.9 + - - +
130A PHE* 3.7 14.6 - - + -
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.1 8.5 + - + +
84A THR 2.6 23.0 + - - -
86A TYR* 1.3 76.9 - - - +
88A THR* 1.3 56.8 + - - +
90A VAL* 3.2 6.2 + - - +
91A GLY* 2.9 22.5 + - - -
130A PHE* 3.3 44.4 - - + +
133A ASP* 2.6 40.3 + - + +
134A LEU* 3.9 10.4 - - + +
137A CYS* 3.7 12.8 - - - -
253A TYR* 3.6 3.6 - - - -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.8 17.5 - - + -
84A THR 3.1 3.3 + - - -
85A ILE 3.5 10.1 - - - -
86A TYR 3.1 0.2 - - - -
87A THR* 1.3 77.2 + - - +
89A LEU* 1.3 68.7 + - - +
91A GLY* 2.6 12.8 + - - +
92A LEU* 2.8 37.2 + - + +
137A CYS* 4.9 1.1 - - - -
252A PRO* 3.0 19.9 - - + +
253A TYR* 2.7 38.0 - - + +
256A PHE* 3.8 10.8 - - + -
260A LEU* 6.3 0.4 - - - -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.0 9.2 - - + -
38A VAL* 5.1 0.9 - - + -
50A LEU* 3.7 28.9 - - + +
53A LEU* 3.4 48.0 - - + -
54A ALA* 4.5 4.7 - - + +
57A LEU* 4.0 12.1 - - + -
72A LEU* 3.7 25.8 - - + -
85A ILE 3.3 6.2 + - - +
86A TYR* 3.6 19.5 - - + +
88A THR* 1.3 80.2 - - - +
90A VAL* 1.3 66.4 + - + +
92A LEU* 3.2 7.6 + - + +
93A LEU* 3.1 26.0 + - + +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.1 23.1 - - + -
86A TYR 2.9 17.5 + - - +
87A THR 3.4 7.2 - - - +
89A LEU* 1.3 75.3 - - - +
91A GLY* 1.3 61.5 - - - +
93A LEU* 3.5 10.7 + - - +
94A ASN* 3.1 20.4 + - - +
100A PHE* 4.9 10.2 - - + -
101A GLY* 5.5 3.0 - - - -
104A PHE* 3.2 50.3 - - + -
130A PHE* 4.2 5.8 - - + -
134A LEU* 4.3 10.3 - - + -
139A VAL* 4.5 6.6 - - + +
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR 2.9 10.6 + - - -
88A THR* 2.6 17.1 + - - -
90A VAL* 1.3 67.3 - - - +
92A LEU* 1.3 55.3 + - - -
93A LEU 3.0 1.3 - - - -
94A ASN* 2.5 27.2 + - - +
95A ALA* 3.0 11.1 + - - +
137A CYS* 4.3 9.4 - - - -
138A HIS 5.5 0.2 - - - +
139A VAL* 4.0 17.7 - - - -
260A LEU* 4.0 11.5 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 5.2 6.1 - - + +
51A GLU* 4.8 6.3 - - - +
54A ALA* 4.3 20.0 - - + -
88A THR* 2.8 42.5 + - + +
89A LEU* 3.7 8.7 - - - +
91A GLY* 1.3 70.9 - - - +
93A LEU* 1.3 63.4 + - + +
95A ALA* 3.4 11.2 + - - +
96A ARG* 3.4 24.9 - - - +
256A PHE* 3.7 44.0 - - + -
259A ILE* 3.8 26.9 - - + -
260A LEU* 4.2 10.1 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 4.0 34.3 - - + +
57A LEU* 4.1 21.3 - - + -
58A GLU* 5.1 8.3 - - + +
61A LEU* 5.7 5.6 - - + -
68A ILE* 5.2 0.4 - - + -
72A LEU* 4.0 17.0 - - + -
89A LEU* 3.1 17.4 + - + +
90A VAL* 3.6 9.2 - - - +
91A GLY 3.0 0.6 - - - -
92A LEU* 1.3 76.9 - - - +
94A ASN* 1.3 56.8 + - - +
96A ARG* 3.2 6.2 + - - +
97A ASN* 2.7 39.8 + - - +
100A PHE* 3.3 39.7 - - + +
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL 3.1 12.2 + - - +
91A GLY 2.5 16.3 + - - +
93A LEU* 1.3 72.7 - - - +
95A ALA* 1.3 55.8 + - - +
96A ARG 2.8 6.9 + - - -
97A ASN 3.1 18.1 + - - -
98A TYR* 3.4 9.9 + - - +
100A PHE* 5.3 0.2 - - - -
101A GLY* 3.1 30.2 + - - +
138A HIS 3.4 20.7 + - - +
139A VAL* 3.6 24.5 - - + +
263A ALA* 4.7 5.4 - - + +
264A LEU 3.8 12.7 + - - +
266A HIS* 3.5 20.7 + - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLY 3.0 9.9 + - - +
92A LEU* 3.5 7.0 - - - +
93A LEU 3.3 0.2 - - - -
94A ASN* 1.3 74.6 - - - +
96A ARG* 1.3 67.1 + - - +
259A ILE* 3.4 38.7 - - + +
260A LEU* 4.6 3.1 - - + -
262A GLU* 5.1 9.0 - - + +
263A ALA* 3.6 25.5 - - + +
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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