Contacts of the helix formed by residues 77 - 93 (chain A) in PDB entry 3ITX
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A PRO 3.5 1.0 - - - -
76A ARG* 1.3 81.0 - - - +
78A ILE* 1.3 65.6 + - - -
79A PHE* 3.3 3.6 - - - -
80A ASP* 3.3 5.1 + - - +
81A LYS* 3.1 33.9 + - - +
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Residues in contact with ILE 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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56A SER* 4.0 11.7 - - - -
77A GLY* 1.3 72.1 - - - -
79A PHE* 1.3 80.1 + - + +
81A LYS* 3.1 9.0 + - + +
82A LEU* 2.8 37.6 + - + +
100A LEU* 3.7 17.9 - - + -
104A TRP 5.5 2.6 + - - -
105A ASP* 3.6 49.7 + - + +
106A LYS 4.7 1.6 - - - +
107A ALA* 4.2 6.1 - - + -
112A LEU* 3.7 30.3 - - + -
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Residues in contact with PHE 79 (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 GLY 3.3 0.8 - - - -
78A ILE* 1.3 91.1 - - + +
80A ASP* 1.3 65.4 + - - +
82A LEU* 3.3 6.5 + - + +
83A ASP* 3.1 15.8 + - - -
107A ALA* 4.1 12.6 - - + -
111A GLU* 3.6 53.6 - - + -
112A LEU* 4.3 14.1 - - + -
115A ARG* 3.1 60.8 + - + +
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Residues in contact with ASP 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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75A PRO* 3.7 9.4 - - + -
76A ARG* 2.9 78.2 + - - +
77A GLY 3.3 5.3 + - - +
79A PHE* 1.3 79.3 - - - +
81A LYS* 1.3 62.9 + - - +
83A ASP* 3.2 12.7 + - - +
84A ASP* 3.0 25.6 + - - -
419A ARG* 3.5 20.3 + - - +
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Residues in contact with LYS 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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56A SER* 3.2 27.3 + - - +
57A TRP* 4.4 11.2 - - - +
59A VAL* 3.5 20.8 - - + +
60A GLY* 5.3 3.8 - - - +
75A PRO* 3.7 24.7 - - + -
77A GLY* 3.1 23.3 + - - +
78A ILE* 3.1 17.2 + - + +
80A ASP* 1.3 77.2 - - - +
82A LEU* 1.3 56.6 + - - +
84A ASP* 3.2 4.7 + - - +
85A CYS* 2.9 34.2 + - - -
104A TRP* 5.2 9.7 + - - +
105A ASP* 4.2 15.7 + - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 5.8 0.2 - - - -
78A ILE* 2.8 39.3 + - + +
79A PHE* 3.7 8.1 - - + +
81A LYS* 1.3 75.2 - - - +
83A ASP* 1.3 63.3 + - - +
85A CYS* 3.1 6.1 + - - +
86A ALA 2.9 18.5 + - - -
98A VAL* 4.1 28.5 - - + -
100A LEU* 4.6 0.2 - - + -
112A LEU* 4.3 17.3 - - + +
115A ARG* 3.8 25.4 - - + -
116A GLY* 4.6 2.9 - - - +
119A LEU* 3.6 15.2 - - + +
121A LEU* 3.5 11.7 - - + +
123A PHE* 4.0 27.4 - - + -
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Residues in contact with ASP 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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5A ARG* 3.4 47.4 + - - +
79A PHE 3.1 15.0 + - - +
80A ASP* 3.2 19.8 + - - +
82A LEU* 1.3 77.2 - - - +
84A ASP* 1.3 61.3 + - - +
86A ALA* 3.2 16.4 + - - +
87A VAL 3.4 4.0 + - - -
115A ARG* 3.2 24.3 + - - -
119A LEU* 3.5 21.0 - - - +
411A TYR* 3.7 2.0 + - - +
419A ARG* 4.3 2.1 + - - +
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Residues in contact with ASP 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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59A VAL* 4.1 11.0 - - + +
75A PRO* 4.0 13.7 - - - +
80A ASP 3.0 12.4 + - - +
81A LYS 3.2 7.2 + - - +
83A ASP* 1.3 72.3 - - - +
85A CYS* 1.3 65.1 + - - +
86A ALA 3.1 1.6 - - - -
87A VAL* 3.0 21.6 + - - +
88A ILE 3.3 4.3 + - - -
336A ILE* 3.4 32.4 - - + +
411A TYR* 2.6 36.0 + - - -
412A ARG* 4.9 3.6 + - - -
419A ARG* 2.8 32.7 + - - -
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Residues in contact with CYS 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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54A VAL* 3.9 23.5 - - + +
55A PRO 4.6 5.2 - - - -
56A SER* 4.7 2.0 - - - -
59A VAL* 3.8 19.3 - - - -
81A LYS 2.9 19.9 + - - -
82A LEU* 3.1 9.4 + - - +
84A ASP* 1.3 76.5 - - - +
86A ALA* 1.3 61.9 + - - +
88A ILE* 3.2 13.0 + - - +
89A GLN* 3.1 22.2 + - - +
95A THR* 4.5 1.7 + - - +
98A VAL* 3.7 34.5 - - + -
121A LEU* 4.0 4.8 - - + +
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Residues in contact with ALA 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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5A ARG* 3.7 16.2 - - + -
82A LEU 2.9 12.1 + - - +
83A ASP 3.3 12.3 - - - +
84A ASP 3.1 0.4 - - - -
85A CYS* 1.3 78.1 - - - +
87A VAL* 1.3 55.8 + - - +
89A GLN* 3.8 1.4 - - - +
90A GLN* 2.9 31.5 + - - +
119A LEU* 3.8 33.2 - - + +
121A LEU* 3.7 11.4 - - + +
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Residues in contact with VAL 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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5A ARG* 3.5 17.7 - - + -
6A ILE* 4.0 8.5 - - + -
83A ASP 3.8 3.4 - - - +
84A ASP 3.0 10.1 + - - +
86A ALA* 1.3 75.7 - - - +
88A ILE* 1.3 65.3 + - - +
90A GLN* 3.4 3.4 + - - +
91A LEU* 3.1 37.4 + - + +
336A ILE* 4.0 11.7 - - + -
406A TYR* 3.9 28.3 - - + -
411A TYR* 3.4 44.4 - - + +
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Residues in contact with ILE 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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54A VAL* 4.3 10.1 - - + -
59A VAL* 4.1 2.0 - - + -
84A ASP 3.6 9.6 - - - +
85A CYS* 3.2 15.2 + - - +
87A VAL* 1.3 77.0 - - - +
89A GLN* 1.3 52.6 + - - +
92A THR* 2.7 44.2 + - + +
95A THR* 3.4 25.4 - - + +
336A ILE* 3.9 31.2 - - + +
339A LEU* 3.5 38.6 - - + +
340A ILE* 4.1 26.0 - - + +
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Residues in contact with GLN 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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51A PHE* 5.9 1.0 - - - -
85A CYS 3.1 8.3 + - - +
86A ALA 3.8 3.1 - - - +
88A ILE* 1.3 75.4 - - - +
90A GLN* 1.3 62.2 + - - +
92A THR* 4.2 0.4 - - - -
93A ARG* 2.6 61.8 + - - +
95A THR* 2.9 44.0 + - - +
96A PRO* 3.1 22.8 - - + +
119A LEU 5.6 2.5 - - - +
120A GLY 4.5 8.4 + - - +
121A LEU* 3.7 24.0 - - + -
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Residues in contact with GLN 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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4A PHE* 3.8 19.4 - - + +
5A ARG* 3.5 16.0 - - - +
6A ILE* 2.8 58.4 - - - +
7A ALA 4.9 0.3 - - - -
8A GLN* 5.0 1.9 + - - +
11A VAL* 4.1 10.4 - - + +
86A ALA 2.9 19.8 + - - +
87A VAL 3.4 3.8 + - - +
89A GLN* 1.3 74.2 - - - +
91A LEU* 1.3 62.4 - - + +
93A ARG* 3.0 40.1 + - - +
397A GLY 3.4 3.3 - - - +
398A GLY* 3.3 11.8 - - - -
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Residues in contact with LEU 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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6A ILE* 4.2 17.0 - - + -
11A VAL* 4.2 21.3 - - + -
87A VAL* 3.1 31.6 + - + +
88A ILE 4.3 0.9 - - - +
90A GLN* 1.3 82.6 - - + +
92A THR* 1.3 60.3 + - - +
340A ILE* 4.1 8.1 - - + -
393A ARG* 3.4 9.7 - - - -
398A GLY* 3.5 1.8 - - - -
399A ALA* 2.9 40.9 + - + +
402A PRO* 3.6 33.5 - - + +
405A THR* 4.2 6.1 - - + -
406A TYR* 3.8 22.0 - - + -
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Residues in contact with THR 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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88A ILE* 2.7 28.1 + - + +
91A LEU* 1.3 77.4 - - - +
93A ARG* 1.3 71.1 + - - +
94A ALA* 3.0 21.5 + - - +
95A THR* 3.8 7.4 + - - +
340A ILE* 3.7 42.8 - - + +
343A ALA* 4.7 2.0 - - + -
344A ASN* 3.9 18.8 + - - +
347A ARG* 3.8 8.0 + - - -
393A ARG* 3.5 21.2 - - - +
402A PRO* 4.4 1.3 - - + -
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Residues in contact with ARG 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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4A PHE* 4.9 13.7 - - - -
48A GLU 4.7 0.7 - - - +
51A PHE* 3.6 13.0 - - - -
89A GLN* 2.6 53.9 + - - +
90A GLN* 3.0 31.4 + - - +
92A THR* 1.3 73.3 + - - +
94A ALA* 1.3 56.3 - - - +
347A ARG* 3.1 15.4 + - - +
393A ARG* 5.1 0.2 - - - -
396A THR* 3.2 51.1 + - + +
397A GLY* 3.0 21.6 + - - -
398A GLY* 3.6 15.3 - - - +
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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
------------------------------------------------------------
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