Contacts of the helix formed by residues 75 - 90 (chain D) in PDB entry 1C03
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 LEU 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ILE 3.8 5.8 - - - +
9D ILE* 4.2 18.2 - - + -
35D PHE* 3.4 39.7 - - + -
70D SER* 2.8 24.5 + - - +
71D ALA* 5.1 0.4 - - - -
73D LEU* 4.0 22.2 - - + +
74D GLY* 1.3 77.6 - - - +
76D GLN* 1.3 60.5 + - - +
77D ARG 3.3 3.0 + - - -
78D ILE* 3.4 17.7 + - + +
79D ALA* 3.3 17.2 + - - +
155D ALA* 4.2 16.2 - - + -
159D LEU* 4.1 27.6 - - + -
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Residues in contact with GLN 76 (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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20B MET* 6.5 0.9 - - - -
5D PRO* 3.5 31.3 - - + +
7D GLU* 2.7 48.2 + - - +
8D ILE 3.5 5.8 + - - +
9D ILE 4.0 4.6 + - - -
10D ASN* 3.8 28.6 - - + +
71D ALA* 5.8 1.3 - - - +
74D GLY 3.1 7.4 + - - +
75D LEU* 1.3 71.8 - - - +
77D ARG* 1.3 61.2 + - - +
78D ILE 3.4 0.2 - - - -
79D ALA* 3.8 9.8 - - - +
80D TRP* 3.2 24.3 + - - +
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Residues in contact with ARG 77 (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 ILE* 3.8 17.9 - - + +
5D PRO* 2.8 28.0 + - + +
6D SER 4.1 1.6 + - - -
7D GLU 3.7 17.3 - - - +
8D ILE* 4.0 18.7 + - + +
75D LEU 3.3 0.4 - - - -
76D GLN* 1.3 77.0 - - - +
78D ILE* 1.3 67.4 + - + +
79D ALA 3.2 0.2 - - - -
80D TRP* 3.6 6.6 + - - +
81D VAL* 3.2 28.0 + - - +
102D LEU 3.1 14.3 + - - -
103D VAL* 5.2 0.8 - - - +
105D THR* 2.5 31.1 + - - -
106D LEU* 3.6 38.4 - - - +
151D GLU* 2.6 59.1 + - + +
154D LEU* 5.1 0.6 - - - +
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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
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35D PHE* 4.1 26.7 - - + -
43D PHE* 5.1 11.0 - - + -
66D LEU* 4.7 6.3 - - + -
70D SER* 4.0 14.4 - - - +
75D LEU* 3.4 16.5 + - + +
77D ARG* 1.3 79.8 - - + +
79D ALA* 1.3 61.5 + - - +
81D VAL* 3.3 5.5 + - - +
82D CYS* 3.1 32.9 + - - -
148D SER* 5.1 4.7 - - - +
151D GLU* 3.9 24.5 - - + +
152D PHE* 3.7 25.8 - - + +
155D ALA* 4.0 15.7 - - + -
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Residues in contact with ALA 79 (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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20B MET* 4.3 15.5 - - + -
67D LYS* 4.0 16.9 - - - +
70D SER* 3.6 18.6 - - - +
71D ALA* 4.2 12.8 - - + -
75D LEU 3.3 11.6 + - - +
76D GLN* 4.0 9.6 - - - +
77D ARG 3.2 0.6 - - - -
78D ILE* 1.3 79.1 - - - +
80D TRP* 1.3 56.9 + - - +
82D CYS* 3.2 7.2 + - - +
83D GLU* 2.9 28.7 + - - +
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Residues in contact with TRP 80 (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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2D SER* 3.4 33.9 - - - -
3D THR* 3.8 12.1 + - - -
4D ILE* 3.5 50.7 - - + +
5D PRO* 4.0 15.0 - - + -
76D GLN 3.2 16.5 + - - +
77D ARG 3.7 3.6 - - - +
79D ALA* 1.3 78.6 - - - +
81D VAL* 1.3 71.2 + - + +
83D GLU* 3.1 15.0 + - - +
84D ARG* 3.1 66.4 + - + +
96D PHE* 4.0 20.0 - + - -
97D PRO* 4.8 2.5 - - + -
102D LEU* 4.3 10.3 - - + -
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Residues in contact with VAL 81 (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 ILE* 4.4 2.2 - - + -
77D ARG 3.2 16.9 + - - +
78D ILE* 3.8 4.5 - - - +
79D ALA 3.3 0.4 - - - -
80D TRP* 1.3 94.5 - - + +
82D CYS* 1.3 57.9 + - - +
84D ARG* 3.1 6.3 + - - +
85D ILE* 2.9 25.9 + - + +
96D PHE* 4.1 14.6 - - + -
144D ALA* 3.2 22.2 - - + +
147D GLN* 4.1 17.5 - - + -
148D SER* 3.2 27.4 - - - +
151D GLU* 4.2 11.4 - - + -
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Residues in contact with CYS 82 (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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43D PHE* 5.6 0.4 - - - -
46D MET* 5.2 0.9 - - - -
63D GLY* 3.5 20.2 - - - +
66D LEU* 3.8 39.9 - - - -
67D LYS* 3.8 10.8 - - + -
78D ILE* 3.1 23.7 + - - +
79D ALA 3.2 8.0 + - - +
81D VAL* 1.3 72.8 - - - +
83D GLU* 1.3 65.6 + - - +
85D ILE* 3.1 14.5 + - - +
86D GLN* 3.0 27.0 + - - +
148D SER* 4.8 7.9 - - - -
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Residues in contact with GLU 83 (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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20B MET* 3.8 16.0 - - - +
23B ASP* 3.3 31.5 - - + +
67D LYS* 3.0 33.1 + - - +
79D ALA 2.9 13.1 + - - +
80D TRP* 3.2 16.2 - - - +
82D CYS* 1.3 77.8 - - - +
84D ARG* 1.3 83.7 + - - +
86D GLN* 3.4 14.0 + - - +
87D ASN* 3.1 27.9 + - - +
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 2.9 23.4 + - - -
2D SER* 5.9 0.7 - - - -
80D TRP* 3.1 75.7 + - + +
81D VAL 3.1 6.3 + - - +
83D GLU* 1.3 97.2 + - - +
85D ILE* 1.3 61.2 + - - +
86D GLN 3.1 0.2 - - - -
87D ASN* 3.5 6.7 + - - +
88D LEU* 2.8 39.5 + - + +
93D GLU* 2.8 45.8 + - - +
95D PHE 6.0 0.9 - - - +
96D PHE* 3.9 23.6 - - + -
97D PRO* 6.2 0.4 - - - -
144D ALA* 5.2 0.2 - - + -
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Residues in contact with ILE 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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46D MET* 4.3 26.5 - - + -
59D LEU* 3.4 26.7 - - + +
63D GLY* 4.4 6.1 - - - -
81D VAL 2.9 16.0 + - - +
82D CYS* 3.1 15.0 + - - +
84D ARG* 1.3 75.5 - - - +
86D GLN* 1.3 61.5 + - - +
88D LEU* 3.5 8.3 + - - +
89D GLY* 3.0 19.2 + - - -
141D ILE* 4.1 24.1 - - + +
144D ALA* 3.6 26.7 - - + -
145D LEU* 4.3 5.8 - - + +
148D SER* 4.0 20.6 - - - +
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Residues in contact with GLN 86 (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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24B ASP* 2.7 26.0 + - - +
60D ASP* 3.1 32.8 - - - +
63D GLY* 3.9 6.9 + - - -
64D HIS* 3.2 26.8 + - - +
67D LYS* 3.3 26.5 - - - +
82D CYS 3.0 13.8 + - - +
83D GLU* 3.5 11.4 + - - +
85D ILE* 1.3 74.0 - - - +
87D ASN* 1.3 62.9 + - - +
89D GLY* 2.9 17.8 + - - -
90D ARG* 3.0 41.6 + - - +
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Residues in contact with ASN 87 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASP* 3.6 29.1 + - - +
83D GLU* 3.1 13.1 + - - +
84D ARG* 3.5 10.3 + - - +
86D GLN* 1.3 79.2 - - - +
88D LEU* 1.3 60.9 + - - +
90D ARG* 3.1 22.5 + - - +
91D LYS 3.0 4.2 + - - -
92D MET* 3.0 35.7 + - + +
93D GLU* 2.8 47.6 + - + +
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Residues in contact with LEU 88 (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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84D ARG* 2.8 28.7 + - + +
85D ILE 3.8 3.6 - - - +
87D ASN* 1.3 76.5 - - - +
89D GLY* 1.3 61.1 + - - +
91D LYS* 3.3 9.2 + - - +
93D GLU* 3.5 29.8 - - + +
94D HIS* 4.5 0.2 - - - -
95D PHE 3.9 18.4 - - - +
96D PHE* 4.4 12.6 - - + -
137D TYR* 3.4 27.4 - - + +
140D LEU* 3.4 50.0 - - + +
141D ILE* 3.8 15.9 - - + +
144D ALA* 4.5 6.1 - - + -
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Residues in contact with GLY 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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56D LEU* 3.4 45.7 - - - +
60D ASP* 5.0 3.0 - - - +
85D ILE 3.0 10.8 + - - -
86D GLN 2.9 8.8 + - - -
88D LEU* 1.3 77.6 - - - +
90D ARG* 1.3 59.1 + - - +
91D LYS* 3.4 2.1 - - - +
141D ILE* 4.0 12.3 - - - +
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Residues in contact with ARG 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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23B ASP 4.0 7.9 + - - -
24B ASP* 3.3 26.4 + - - +
25B SER 5.4 0.6 - - - +
60D ASP* 2.8 31.8 + - - +
86D GLN* 3.0 39.0 + - - +
87D ASN* 3.1 23.7 + - - +
89D GLY* 1.3 76.9 - - - +
91D LYS* 1.3 71.4 + - - +
92D MET* 3.1 24.8 + - + +
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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
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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