Contacts of the helix formed by residues 65 - 80 (chain B) in PDB entry 1C3B
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 VAL 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.3 17.7 + - + +
63B GLY 3.1 2.2 + - - -
64B SER* 1.3 79.0 - - - +
66B SER* 1.3 58.7 + - - +
67B LYS 3.1 0.2 - - - -
68B THR* 2.5 43.6 + - + +
69B PHE* 3.9 3.5 - - + -
230B MET* 4.3 15.0 - - + -
233B TRP* 5.1 0.9 - - - +
271B TRP* 5.6 0.2 - - + -
315B LYS* 3.5 31.4 - - + +
316B THR 3.9 0.9 - - - -
317B GLY* 3.8 8.2 - - - +
324B SER* 3.2 24.9 - - - +
326B VAL* 4.0 26.0 - - + -
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 4.2 3.1 - - - +
63B GLY 2.8 19.5 + - - -
65B VAL* 1.3 80.0 - - - +
67B LYS* 1.3 57.3 + - - +
69B PHE* 2.8 33.9 + - - +
70B THR* 3.0 14.2 + - - -
218B ALA 5.1 2.7 - - - -
220B ALA 4.2 1.1 - - - -
221B TYR* 3.4 19.6 + - - -
222B GLY 4.0 0.7 - - - -
223B VAL* 3.0 41.7 + - - +
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 2.6 35.7 + - - +
66B SER* 1.3 78.5 - - - +
68B THR* 1.3 55.1 + - - +
70B THR* 3.4 10.6 + - - -
71B GLY 2.9 22.5 + - - -
112B TYR* 3.4 17.7 - - - +
150B TYR* 3.4 26.4 + - - +
151B ALA 4.7 2.0 - - - -
152B ASN* 2.6 29.9 + - - +
155B ILE* 3.7 35.3 - - + +
219B GLU 4.9 0.4 - - - -
220B ALA* 3.0 25.3 + - - +
270B GLY* 3.4 17.3 - - - +
315B LYS* 3.6 9.2 - - + +
362B BZB 4.1 0.6 - - - +
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 2.5 25.4 + - + +
67B LYS* 1.3 73.8 - - - +
69B PHE* 1.3 61.9 + - - +
71B GLY* 3.4 0.9 + - - -
72B VAL* 3.1 34.0 + - - +
233B TRP* 3.3 18.7 + - - -
269B LEU 4.6 1.9 - - - +
270B GLY* 4.2 12.6 - - - -
271B TRP* 3.4 50.0 + - + -
315B LYS* 3.8 21.5 - - + -
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.8 23.3 - - + -
65B VAL* 3.9 11.9 - - + -
66B SER* 2.8 14.7 + - - +
68B THR* 1.3 79.7 + - - +
70B THR* 1.3 60.9 + - - +
72B VAL* 3.2 2.1 + - - +
73B LEU* 2.8 30.3 + - - +
174B MET* 3.8 18.9 - - + +
178B VAL* 4.2 6.7 - - + +
179B PHE* 3.6 29.6 - + - -
184B LEU* 3.9 11.0 - - + -
187B THR* 4.5 6.3 - - + -
223B VAL* 4.4 11.4 - - + -
230B MET* 4.2 9.6 - - + -
233B TRP* 3.5 62.1 - + + -
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 3.0 10.0 + - - -
67B LYS* 3.6 9.9 - - - -
69B PHE* 1.3 78.6 - - - +
71B GLY* 1.3 61.2 + - - +
73B LEU* 3.4 3.3 + - - +
74B GLY* 3.0 19.4 + - - -
155B ILE* 4.2 17.9 - - + +
158B PHE* 4.1 6.1 - - + -
159B GLY* 3.8 28.4 - - - +
170B PHE* 3.6 13.1 - - + -
174B MET* 4.1 8.2 - - - +
218B ALA 4.6 1.2 + - - -
219B GLU 2.6 31.7 + - - +
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS 2.9 13.3 + - - -
69B PHE 3.2 0.4 - - - -
70B THR* 1.3 76.5 - - - +
72B VAL* 1.3 58.4 + - - +
74B GLY* 3.3 1.9 + - - -
75B GLY* 2.8 23.0 + - - -
155B ILE* 5.3 2.7 - - - -
158B PHE* 4.8 6.0 - - - -
255B ALA* 4.1 2.7 - - - +
269B LEU* 3.6 43.7 - - - +
270B GLY 4.5 0.2 - - - -
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR 3.1 20.8 + - - +
69B PHE 3.9 2.2 - - - +
71B GLY* 1.3 75.0 - - - +
73B LEU* 1.3 66.1 + - - +
75B GLY* 3.2 0.9 + - - +
76B ASP* 2.9 21.8 + - - +
178B VAL* 4.8 3.6 - - + -
233B TRP* 3.8 24.7 - - + -
237B ASN* 4.2 0.9 - - - +
248B LEU* 3.8 20.0 - - + -
251B GLY* 4.4 1.6 - - - -
252B ILE* 3.7 34.8 - - + +
255B ALA* 3.6 23.3 - - + -
271B TRP* 4.1 10.8 - - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE 2.8 17.1 + - - +
70B THR 3.7 4.7 - - - +
72B VAL* 1.3 76.2 - - - +
74B GLY* 1.3 62.1 - - - +
76B ASP* 3.2 8.3 + - - +
77B ALA* 3.1 22.3 + - + +
159B GLY 5.6 0.2 - - - +
162B ALA* 6.0 2.2 - - + -
163B VAL* 3.8 20.9 - - + -
170B PHE* 3.7 30.1 - - + -
173B ALA* 3.9 25.6 - - + +
174B MET* 3.7 28.3 - - + +
177B ARG* 4.1 14.1 - - + +
178B VAL* 4.0 17.5 - - + +
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Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR 3.0 14.4 + - - -
71B GLY 3.6 4.0 - - - -
72B VAL 3.1 0.2 - - - -
73B LEU* 1.3 74.4 - - - +
75B GLY* 1.3 65.5 + - - +
77B ALA* 3.1 13.4 + - - +
78B ILE* 3.1 21.5 + - - +
83B ILE* 4.0 1.0 - - - +
158B PHE* 3.9 22.2 - - - -
162B ALA* 4.5 12.8 - - - -
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLY 2.8 15.5 + - - -
72B VAL 3.2 3.1 + - - -
74B GLY* 1.3 76.4 - - - +
76B ASP* 1.3 60.7 + - - +
78B ILE* 3.2 15.5 + - - +
79B ALA* 3.1 18.4 + - - +
251B GLY* 3.4 22.1 - - - -
254B LEU* 3.6 14.7 - - - +
269B LEU* 4.3 3.7 - - - +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL 2.9 12.6 + - - +
73B LEU* 3.4 13.5 - - + +
75B GLY* 1.3 75.7 - - - +
77B ALA* 1.3 58.3 + - - +
79B ALA* 3.2 3.8 + - - +
80B ARG* 2.5 60.1 + - - +
177B ARG* 3.9 17.6 + - + +
178B VAL* 5.7 0.4 - - + -
247B THR* 2.6 45.3 + - - +
248B LEU* 3.2 17.3 + - + +
251B GLY* 3.6 1.4 - - - -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 3.1 14.0 + - + +
74B GLY* 3.1 10.9 + - - +
76B ASP* 1.3 78.1 + - - +
78B ILE* 1.3 58.9 + - - +
80B ARG* 3.4 4.0 + - - +
81B GLY 3.3 2.1 + - - -
82B GLU* 2.9 48.6 + - + +
83B ILE* 3.4 14.9 + - + -
162B ALA* 3.9 20.2 - - + +
163B VAL* 6.4 0.4 - - + -
177B ARG* 4.6 3.6 - - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A THR* 5.7 1.6 - - + +
306A PRO* 3.7 36.7 - - + +
74B GLY 3.1 19.1 + - - +
75B GLY* 3.5 15.0 - - - +
76B ASP 3.2 0.2 - - - -
77B ALA* 1.3 77.7 - - - +
79B ALA* 1.3 58.8 + - - +
81B GLY* 2.9 19.4 + - - -
83B ILE* 3.5 35.1 - - + +
84B LYS* 5.1 3.4 - - - -
85B LEU* 3.7 39.5 - - + +
158B PHE* 5.2 0.7 - - + -
254B LEU* 3.9 10.3 - - + -
269B LEU* 4.6 6.3 - - + -
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO* 5.7 4.9 - - + -
75B GLY 3.1 10.3 + - - +
76B ASP 3.7 6.7 - - - +
78B ILE* 1.3 73.5 - - - +
80B ARG* 1.3 59.9 + - - +
81B GLY* 3.0 6.8 + - - -
247B THR* 3.7 28.3 - - - +
250B GLN* 3.2 35.0 - - + +
254B LEU* 4.4 4.4 - - + +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASP* 2.5 37.6 + - - +
77B ALA* 3.6 7.2 - - - +
78B ILE 3.1 0.2 - - - -
79B ALA* 1.3 76.6 - - - +
81B GLY* 1.3 61.1 + - - +
82B GLU* 3.4 16.7 + - - +
177B ARG* 3.0 66.3 + - - +
245B GLU* 4.8 9.7 + - - -
247B THR* 3.6 29.1 + - + +
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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
------------------------------------------------------------
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