Contacts of the helix formed by residues 75 - 90 (chain A) in PDB entry 1ISR
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 GLY 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 4.6 1.4 - - - +
52A SER 3.2 13.2 + - - -
53A VAL* 3.8 10.8 - - - -
71A ARG* 3.7 9.8 + - - +
72A GLU 3.3 5.1 + - - -
73A GLN 3.3 0.4 - - - -
74A TYR* 1.3 79.8 - - - +
76A ILE* 1.3 67.4 + - - +
77A GLN 3.3 0.9 - - - -
78A ARG* 3.2 6.6 + - - +
79A VAL* 3.1 28.6 + - - +
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Residues in contact with ILE 76 (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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53A VAL* 4.4 4.3 - - + -
70A ILE* 3.7 20.4 - - + -
71A ARG 3.2 18.6 + - - +
72A GLU* 3.4 3.3 + - + +
75A GLY* 1.3 71.0 - - - +
77A GLN* 1.3 57.9 + - - +
79A VAL* 3.2 5.1 + - - +
80A GLU* 2.9 36.3 + - + +
354A PHE* 4.2 12.3 - - + -
365A ASN* 4.5 9.0 - - - +
367A TRP* 3.9 22.7 - - + +
368A PHE* 4.3 9.4 - - + -
371A PHE* 3.5 53.8 - - + -
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Residues in contact with GLN 77 (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 GLU* 2.9 30.5 + - + +
73A GLN* 2.8 51.9 - - - +
76A ILE* 1.3 76.0 - - - +
78A ARG* 1.3 57.8 + - - +
81A ALA* 2.9 28.2 + - - +
350A PHE* 3.4 19.4 - - + -
354A PHE* 4.0 16.4 - - + -
404A TYR* 4.0 7.7 + - - -
405A VAL 3.4 6.3 + - - -
406A GLN* 3.6 7.4 - - - -
407A ASP 3.1 22.1 + - - -
410A MET* 3.6 17.2 - - + +
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Residues in contact with ARG 78 (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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51A PHE* 3.6 34.5 - - + -
52A SER* 5.4 2.6 - - - +
73A GLN 3.7 9.4 - - - +
74A TYR* 3.3 67.5 + - - +
75A GLY 3.2 8.1 + - - +
77A GLN* 1.3 76.0 - - + +
79A VAL* 1.3 65.6 + - - +
80A GLU 3.2 0.2 - - - -
81A ALA* 3.4 6.6 + - - +
82A MET* 3.0 22.5 + - - +
110A TRP* 4.7 5.9 - - - -
163A GLY* 5.0 1.0 - - - -
185A TYR* 3.3 31.1 + - - -
186A SER* 4.7 1.2 + - - -
407A ASP* 2.8 28.9 + - - +
409A LYS* 4.3 16.0 - - - +
410A MET* 5.0 2.0 - - + -
413A VAL* 4.1 16.9 - - + +
1001A GLU* 4.8 0.4 + - - -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 4.3 2.2 - - + -
51A PHE* 4.3 15.7 - - + -
53A VAL* 4.4 7.9 - - + -
75A GLY 3.1 19.5 + - - +
76A ILE* 3.2 5.1 + - - +
78A ARG* 1.3 76.7 - - - +
80A GLU* 1.3 61.3 + - - +
82A MET* 3.2 19.6 + - - +
83A PHE* 3.4 18.5 + - + -
105A ILE* 3.7 19.2 - - + +
365A ASN* 3.2 25.8 - - - +
367A TRP* 3.8 31.4 - - + -
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Residues in contact with GLU 80 (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 ILE* 2.9 24.8 + - + +
77A GLN 3.8 4.0 - - - +
79A VAL* 1.3 74.0 - - - +
81A ALA* 1.3 57.0 + - - +
82A MET 3.0 5.1 + - - -
83A PHE* 3.3 8.0 + - - +
84A HIS* 2.9 30.3 + - - +
350A PHE* 4.1 7.6 - - + -
353A TYR* 2.8 39.1 + - + -
354A PHE* 3.9 11.7 - - + -
357A LEU* 3.2 24.3 - - + +
362A ASN* 3.2 23.0 + - - -
365A ASN* 2.9 27.7 + - - +
368A PHE* 4.5 2.1 - - - -
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Residues in contact with ALA 81 (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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77A GLN 2.9 19.7 + - - +
78A ARG* 3.4 6.9 + - - +
80A GLU* 1.3 75.2 - - - +
82A MET* 1.3 58.9 + - - +
84A HIS* 4.1 5.3 - - - +
85A THR* 2.8 30.3 + - - -
350A PHE* 3.6 14.5 - - + -
410A MET* 3.5 26.2 - - - -
413A VAL* 4.7 7.9 - - + -
414A ILE* 4.9 7.4 - - + -
417A ILE* 3.8 4.0 - - - +
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Residues in contact with MET 82 (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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47A ILE* 5.4 10.8 - - + +
49A ALA* 4.2 21.3 - - - -
51A PHE* 4.2 9.9 - - + -
78A ARG 3.0 12.6 + - - +
79A VAL 3.2 12.1 - - - +
80A GLU 3.0 0.2 - - - -
81A ALA* 1.3 78.3 - - - +
83A PHE* 1.3 65.2 + - - +
85A THR* 3.9 0.3 - - - -
86A LEU* 3.1 49.7 + - + +
103A SER* 4.7 5.4 - - - -
105A ILE* 3.5 28.0 - - + -
160A ILE* 5.0 4.7 - - + -
417A ILE* 3.5 45.1 - - + -
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Residues in contact with PHE 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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39A ALA* 3.8 17.9 - - + -
40A ARG 4.4 12.6 - - - -
41A MET* 3.9 15.9 - - + +
79A VAL* 3.4 18.1 + - + -
80A GLU* 3.3 16.0 + - - +
82A MET* 1.3 77.1 - - - +
84A HIS* 1.3 68.7 + - - +
86A LEU* 3.0 7.5 + - + +
87A ASP* 2.9 28.6 + - - +
103A SER* 3.8 16.8 - - - -
105A ILE* 3.6 19.5 - - + -
353A TYR* 4.4 0.9 - - - +
364A ARG* 3.5 70.9 - - + +
365A ASN* 4.1 9.0 - - + -
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Residues in contact with HIS 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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80A GLU 2.9 17.8 + - - +
81A ALA* 4.1 6.1 - - - +
83A PHE* 1.3 78.3 - - - +
85A THR* 1.3 67.1 + - - +
87A ASP* 3.3 12.2 + - - +
88A LYS* 3.2 45.4 + - + +
349A SER* 3.3 28.2 + - - -
350A PHE* 4.6 14.6 - + + -
353A TYR* 3.3 51.4 - + + +
364A ARG* 4.4 0.6 - - - +
414A ILE* 6.1 4.3 - - + -
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Residues in contact with THR 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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81A ALA 2.8 22.3 + - - -
82A MET 3.9 0.7 - - - -
83A PHE 3.3 0.6 - - - -
84A HIS* 1.3 80.3 - - - +
86A LEU* 1.3 58.1 + - - +
88A LYS* 3.2 13.0 + - + +
89A ILE* 2.9 34.7 + - + +
414A ILE* 3.7 19.7 - - + +
417A ILE* 3.7 34.3 - - + +
418A TYR* 3.4 34.1 - - + -
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Residues in contact with LEU 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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41A MET* 3.9 17.5 - - - -
47A ILE* 4.8 4.7 - - + -
82A MET* 3.1 37.7 - - + +
83A PHE* 3.0 7.5 + - - +
85A THR* 1.3 73.6 - - - +
87A ASP* 1.3 58.6 + - - +
89A ILE* 3.2 4.1 + - + +
90A ASN* 2.7 46.9 + - - +
101A LEU* 4.0 30.7 - - + +
102A GLY 4.1 6.3 - - - +
103A SER* 3.4 35.7 - - - +
417A ILE* 4.3 10.5 - - + -
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Residues in contact with ASP 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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41A MET* 4.0 7.3 - - - +
83A PHE 2.9 18.7 + - - +
84A HIS* 3.5 11.3 + - - +
85A THR 3.3 0.2 - - - -
86A LEU* 1.3 76.0 - - - +
88A LYS* 1.3 58.5 + - + +
90A ASN* 3.4 7.7 + - - +
91A ALA* 3.0 30.4 + - - +
353A TYR* 5.2 1.2 - - - -
364A ARG* 2.8 43.0 + - - -
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Residues in contact with LYS 88 (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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84A HIS* 3.3 40.8 - - + +
85A THR* 3.4 11.9 - - + +
86A LEU 3.1 0.6 - - - -
87A ASP* 1.3 78.7 - - + +
89A ILE* 1.3 56.8 + - - +
91A ALA* 3.1 6.8 + - - +
92A ASP* 2.9 29.4 + - - +
348A ARG* 5.6 2.0 - - - +
349A SER* 3.8 20.3 + - - -
418A TYR* 4.3 21.0 + - + +
462A VAL* 4.6 15.0 - - - +
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Residues in contact with ILE 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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85A THR* 2.9 35.9 + - + +
86A LEU* 3.8 7.0 - - + +
88A LYS* 1.3 76.5 - - - +
90A ASN* 1.3 62.0 + - - +
91A ALA 3.1 1.0 + - - -
92A ASP* 3.4 15.4 + - - +
95A LEU* 3.6 44.3 - - + +
96A LEU* 4.2 10.5 - - + +
99A ILE 5.4 0.7 - - - +
101A LEU* 3.9 26.9 - - + -
417A ILE* 4.0 15.0 - - + -
418A TYR* 4.4 14.6 - - + -
421A ALA* 4.1 15.9 - - + -
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Residues in contact with ASN 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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41A MET* 4.9 5.1 - - - -
86A LEU* 2.7 33.1 + - - +
87A ASP* 3.7 7.1 + - - +
89A ILE* 1.3 77.9 - - - +
91A ALA* 1.3 58.1 + - - +
92A ASP 3.5 2.1 - - - +
96A LEU 6.0 0.2 - - - -
99A ILE 3.9 5.7 - - - +
100A THR* 3.2 22.3 - - + +
101A LEU* 2.7 50.0 + - - +
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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