Contacts of the helix formed by residues 77 - 93 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PRO 3.8 3.0 + - - -
76D ARG* 1.3 75.7 - - - +
78D ILE* 1.3 64.3 + - - -
79D PHE 3.3 3.7 + - - -
80D ASP 3.3 0.5 + - - -
81D LYS* 3.1 35.4 + - - +
104D TRP 5.6 3.1 - - - -
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Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D SER* 5.2 1.3 - - - -
77D GLY* 1.3 71.2 - - - -
79D PHE* 1.3 71.2 + - + +
81D LYS* 3.2 12.0 + - + +
82D LEU* 2.8 40.6 + - + +
100D LEU* 3.4 26.0 - - + -
104D TRP 5.1 3.0 + - - -
105D ASP* 3.4 53.6 + - + +
106D LYS 5.2 0.2 - - - +
107D ALA* 4.2 7.4 - - + -
112D LEU* 3.2 33.2 - - + -
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Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG 5.8 0.7 - - - +
77D GLY 3.3 1.0 - - - -
78D ILE* 1.3 82.0 - - + +
80D ASP* 1.3 64.5 + - - +
82D LEU* 3.4 6.5 + - + +
83D ASP* 3.1 18.6 + - - -
107D ALA* 4.1 18.4 - - + -
111D GLU* 3.7 52.5 - - + -
112D LEU* 4.0 21.3 - - + -
115D ARG* 3.3 56.1 + - + +
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PRO* 3.6 9.8 - - + +
76D ARG* 2.8 52.7 + - - +
77D GLY 3.3 4.0 + - - +
79D PHE* 1.3 79.1 - - - +
81D LYS* 1.3 63.3 + - - +
83D ASP* 3.2 13.9 + - - +
84D ASP* 3.0 19.2 + - - -
419D ARG* 3.5 32.5 + - - +
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Residues in contact with LYS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D SER* 3.2 31.2 + - - +
57D TRP* 4.5 10.9 - - - +
59D VAL* 3.3 24.6 - - + +
60D GLY* 5.4 3.8 - - - +
75D PRO* 3.9 18.4 - - + -
77D GLY* 3.1 29.2 + - - +
78D ILE* 3.4 12.1 - - + +
79D PHE 3.2 0.2 - - - -
80D ASP* 1.3 78.4 - - - +
82D LEU* 1.3 57.6 + - + +
84D ASP* 3.2 4.0 + - - +
85D CYS* 2.8 33.7 + - - -
104D TRP* 5.2 10.3 + - - +
105D ASP* 4.2 14.6 + - - +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D SER* 5.8 0.4 - - - -
78D ILE* 2.8 39.0 + - + +
79D PHE* 3.8 9.4 - - + +
81D LYS* 1.3 74.0 - - + +
83D ASP* 1.3 57.5 + - - +
85D CYS* 3.1 3.6 + - - -
86D ALA* 2.9 27.5 + - - +
98D VAL* 4.2 28.3 - - + -
100D LEU* 4.6 1.1 - - + -
112D LEU* 4.4 20.9 - - + +
115D ARG* 3.9 25.1 - - + -
116D GLY* 4.8 2.7 - - - +
119D LEU* 3.7 13.0 - - + -
121D LEU* 3.5 13.3 - - + +
123D PHE* 4.1 22.7 - - + -
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Residues in contact with ASP 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 3.3 49.8 + - - +
79D PHE 3.1 16.6 + - - +
80D ASP* 3.3 17.9 - - - +
82D LEU* 1.3 77.4 - - - +
84D ASP* 1.3 60.1 + - - +
86D ALA* 3.3 15.6 - - - +
87D VAL* 3.6 1.9 + - - +
115D ARG* 3.5 20.7 + - - -
119D LEU* 3.5 21.7 - - - +
411D TYR* 3.5 3.3 + - - +
419D ARG* 4.3 3.6 + - - +
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Residues in contact with ASP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D VAL* 3.2 27.6 - - + +
73D GLY 4.8 0.2 - - - +
75D PRO* 3.6 15.6 - - - +
80D ASP 3.0 9.3 + - - -
81D LYS 3.6 2.5 - - - +
83D ASP* 1.3 74.1 - - - +
85D CYS* 1.3 64.3 + - - +
86D ALA 3.1 0.4 - - - -
87D VAL* 3.0 21.0 + - - +
88D ILE 3.5 3.3 + - - -
336D ILE* 3.5 18.9 - - + +
411D TYR* 2.6 37.2 + - - -
412D ARG* 4.9 4.9 + - - -
419D ARG* 2.9 33.4 + - - -
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Residues in contact with CYS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D VAL* 3.9 25.0 - - + +
55D PRO 4.8 1.1 - - - -
56D SER* 4.8 8.1 - - - -
59D VAL* 4.6 14.1 - - - -
81D LYS 2.8 26.3 + - - +
82D LEU* 3.5 6.1 - - - +
84D ASP* 1.3 75.2 - - - +
86D ALA* 1.3 62.3 + - - +
88D ILE* 3.1 24.9 + - - +
89D GLN* 3.1 14.2 + - - +
95D THR* 4.6 1.2 + - - +
98D VAL* 3.8 33.9 - - + -
121D LEU* 4.0 4.5 - - + +
339D LEU* 5.8 0.2 - - - -
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 3.6 16.3 - - + +
82D LEU 2.9 11.9 + - - +
83D ASP 3.3 13.0 - - - +
84D ASP 3.1 0.2 - - - -
85D CYS* 1.3 78.0 - - - +
87D VAL* 1.3 55.4 + - - +
89D GLN* 3.5 2.5 + - - +
90D GLN* 2.9 30.3 + - - +
119D LEU* 3.9 33.4 - - + +
121D LEU* 3.7 11.2 - - - +
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 3.4 27.6 - - + -
6D ILE* 4.0 9.0 - - + -
83D ASP 3.8 2.2 - - - +
84D ASP 3.0 11.0 + - - +
86D ALA* 1.3 76.2 - - - +
88D ILE* 1.3 65.6 + - - +
90D GLN* 3.3 5.1 + - - +
91D LEU* 3.0 37.2 + - + +
336D ILE* 4.0 10.3 - - + -
406D TYR* 3.9 28.5 - - + -
411D TYR* 3.4 31.9 - - + -
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Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 4.3 11.0 - - + -
59D VAL* 5.3 0.2 - - + -
84D ASP 3.8 7.2 - - - +
85D CYS* 3.1 18.3 + - - +
87D VAL* 1.3 77.3 - - - +
89D GLN* 1.3 52.7 + - - +
92D THR* 2.8 41.0 + - + +
95D THR* 3.3 25.8 - - + +
336D ILE* 3.8 29.8 - - + +
339D LEU* 3.5 39.5 - - + +
340D ILE* 3.3 29.8 - - + +
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Residues in contact with GLN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PHE* 5.8 1.0 - - - -
85D CYS 3.1 5.1 + - - -
86D ALA 3.9 4.9 - - - +
88D ILE* 1.3 76.0 - - - +
90D GLN* 1.3 63.0 + - - +
93D ARG* 2.7 62.4 + - - +
95D THR* 3.0 44.5 + - - +
96D PRO* 3.0 26.7 - - + +
119D LEU 5.4 2.7 - - - +
120D GLY 4.2 10.3 + - - +
121D LEU* 3.8 18.6 - - + -
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Residues in contact with GLN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 3.9 21.1 - - + +
5D ARG* 3.5 12.8 + - - +
6D ILE* 2.9 57.3 + - - +
7D ALA 5.0 0.2 - - - -
8D GLN* 5.1 1.8 - - - +
11D VAL* 3.8 16.2 - - - +
86D ALA 2.9 17.5 + - - +
87D VAL 3.7 4.3 - - - +
89D GLN* 1.3 77.6 - - - +
91D LEU* 1.3 59.3 + - + +
93D ARG* 3.0 39.0 + - - +
397D GLY 3.5 2.6 - - - +
398D GLY* 3.3 11.8 - - - -
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.4 14.6 - - + -
11D VAL* 4.3 15.5 - - + -
87D VAL* 3.0 30.8 + - + +
88D ILE 4.3 1.3 - - - +
90D GLN* 1.3 82.1 - - + +
92D THR* 1.3 58.6 + - - +
340D ILE* 4.3 7.9 - - + -
393D ARG* 3.5 8.7 - - - -
398D GLY* 3.4 2.9 - - - -
399D ALA* 2.9 34.2 + - + +
402D PRO* 3.6 33.8 - - + +
405D THR* 4.0 22.2 - - + -
406D TYR* 3.8 23.1 - - + +
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Residues in contact with THR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ILE* 2.8 19.0 + - + +
91D LEU* 1.3 77.2 - - - +
93D ARG* 1.3 71.1 + - - +
94D ALA* 3.0 20.2 + - - +
95D THR* 3.9 8.1 + - - +
340D ILE* 3.2 50.3 - - + +
343D ALA* 4.8 2.2 - - + -
344D ASN* 3.8 20.3 + - - +
347D ARG* 3.9 8.1 + - - -
393D ARG* 3.5 21.1 - - - +
402D PRO* 4.3 2.2 - - + -
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Residues in contact with ARG 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 4.9 11.7 - - - -
48D GLU 4.9 0.2 - - - +
51D PHE* 3.5 14.0 - - - -
89D GLN* 2.7 53.7 + - - +
90D GLN* 3.0 34.2 + - - +
92D THR* 1.3 75.0 + - - +
94D ALA* 1.3 55.5 + - - +
347D ARG* 3.2 15.9 + - - +
393D ARG* 4.5 0.4 - - - +
396D THR* 3.2 48.2 + - - +
397D GLY* 3.1 22.8 + - - -
398D GLY* 3.6 13.2 - - - +
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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