Contacts of the helix formed by residues 61 - 72 (chain B) in PDB entry 7CAL
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 ALA 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ASN* 5.5 1.3 - - - +
57B PRO 3.4 19.1 + - - +
58B ARG 5.5 0.2 - - - -
59B TYR 3.2 0.2 - - - -
60B ARG* 1.3 77.6 - - - +
62B TRP* 1.3 62.5 + - - +
63B GLU 3.3 0.9 - - - -
64B MET* 3.6 8.3 + - - +
65B TRP* 3.4 19.9 + - - +
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Residues in contact with TRP 62 (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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58B ARG 3.9 17.9 + - - +
59B TYR* 3.5 19.2 + + - +
61B ALA* 1.3 78.9 - - - +
63B GLU* 1.3 68.2 + - + +
65B TRP* 3.2 32.7 + + + +
66B LEU* 3.2 26.0 + - + +
101B PHE* 4.0 29.2 - + - -
104B ILE* 4.1 24.0 - - + -
105B ASP* 2.4 43.8 + - + -
108B LEU* 3.4 23.2 - - + +
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PRO* 5.4 1.6 - - - +
59B TYR* 3.0 55.3 + - + +
60B ARG* 4.6 12.2 - - - +
61B ALA 3.3 0.2 - - - -
62B TRP* 1.3 82.8 - - + +
64B MET* 1.3 62.2 + - + +
65B TRP 3.5 0.3 + - - -
66B LEU* 3.6 8.7 + - + +
67B VAL* 3.4 25.6 + - - +
105B ASP* 5.8 1.1 - - - +
177B ARG* 5.6 8.2 + - - +
181B LEU* 5.4 1.1 - - + +
184B ARG* 3.7 31.4 + - - +
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 3.9 20.2 + - - +
61B ALA* 3.6 9.7 + - - +
62B TRP 3.3 0.4 - - - -
63B GLU* 1.3 79.6 - - + +
65B TRP* 1.3 61.2 + - - +
67B VAL* 3.8 17.9 + - - +
68B LEU* 3.9 13.7 + - - +
181B LEU* 4.2 29.4 - - + -
184B ARG* 5.7 4.3 - - - +
185B LEU* 6.1 4.7 - - + -
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Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA 3.4 11.6 + - - +
62B TRP* 3.2 28.6 + + + +
63B GLU 3.2 0.8 - - - -
64B MET* 1.3 77.3 - - - +
66B LEU* 1.3 67.3 + - + +
67B VAL 3.2 2.0 - - - -
68B LEU* 3.2 29.0 + - + +
69B LEU* 3.4 34.7 + - + +
101B PHE* 3.4 53.6 - + + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TRP* 3.2 28.7 + - + +
63B GLU* 3.6 9.4 + - + +
64B MET 3.5 0.2 - - - -
65B TRP* 1.3 77.7 - - + +
67B VAL* 1.3 64.3 + - + +
69B LEU* 3.3 17.5 + - + +
70B VAL* 3.3 26.3 + - - +
101B PHE* 3.9 19.5 - - + +
102B PHE* 3.9 24.1 - - + -
105B ASP* 3.4 40.2 - - + +
177B ARG* 4.4 23.3 - - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU 3.4 16.5 + - - +
64B MET* 3.9 16.4 - - - +
65B TRP 3.2 0.6 - - - -
66B LEU* 1.3 78.3 - - - +
68B LEU* 1.3 61.3 + - + +
70B VAL* 3.0 20.5 + - - +
71B ILE* 3.1 27.4 + - + +
177B ARG* 4.2 17.7 - - + +
178B VAL* 4.0 17.5 - - + -
181B LEU* 3.7 33.2 - - + -
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Residues in contact with LEU 68 (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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64B MET 4.1 12.1 - - - +
65B TRP* 3.2 24.9 + - + +
67B VAL* 1.3 79.6 - - + +
69B LEU* 1.3 64.2 + - + +
71B ILE* 4.1 21.6 - - + +
72B TYR* 3.5 23.4 + - - +
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Residues in contact with LEU 69 (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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65B TRP* 3.4 54.0 + - + +
66B LEU* 3.3 11.8 + - + +
67B VAL 3.2 1.0 - - - -
68B LEU* 1.3 83.8 - - + +
70B VAL* 1.3 59.4 + - - +
72B TYR* 4.6 7.0 - - + -
73B SER* 3.3 25.0 + - - -
98B VAL* 4.0 27.4 - - + +
101B PHE* 4.0 22.0 - - + -
102B PHE* 3.6 23.2 - - + -
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Residues in contact with VAL 70 (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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66B LEU 3.3 14.6 - - - +
67B VAL 3.0 8.3 + - - +
69B LEU* 1.3 78.2 - - - +
71B ILE* 1.3 59.6 + - - +
72B TYR 3.2 0.9 - - - -
73B SER* 3.5 3.9 - - - +
74B ALA* 2.9 30.5 + - + +
102B PHE* 3.6 21.3 - - + -
174B ARG* 3.3 35.2 - - + +
175B LEU* 3.7 24.9 - - + -
177B ARG* 4.2 9.6 - - + -
178B VAL* 3.7 17.5 - - + -
701B 3PE 6.4 0.2 - - + -
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Residues in contact with ILE 71 (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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67B VAL* 3.1 29.1 + - + +
68B LEU* 4.3 20.9 - - + +
70B VAL* 1.3 78.1 - - - +
72B TYR* 1.3 60.9 + - - +
74B ALA* 4.1 1.4 - - - +
75B TRP* 3.5 19.4 + - - +
178B VAL* 4.5 13.7 - - + -
701B 3PE 4.1 34.0 - - + +
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Residues in contact with TYR 72 (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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68B LEU 3.5 17.5 + - - +
69B LEU* 4.6 5.6 - - + -
70B VAL 3.2 0.6 - - - -
71B ILE* 1.3 78.9 - - - +
73B SER* 1.3 64.3 + - - +
74B ALA 3.1 0.4 - - - -
75B TRP* 3.0 20.3 + + + +
76B ILE* 3.3 57.8 + - + +
91B ILE* 4.0 15.9 - - + +
94B ILE* 3.4 39.5 - - + +
95B ASP* 4.8 1.1 + - - -
98B VAL* 4.2 22.9 - - + -
171B ARG* 5.7 0.4 - - - -
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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