Contacts of the helix formed by residues 61 - 72 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASN* 4.8 2.0 + - - +
57A PRO 3.4 18.4 + - - +
59A TYR 3.2 0.2 - - - -
60A ARG* 1.3 78.1 - - - +
62A TRP* 1.3 62.0 + - - +
63A GLU 3.3 0.9 - - - -
64A MET* 3.6 8.1 + - - +
65A TRP* 3.4 19.6 + - - +
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Residues in contact with TRP 62 (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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58A ARG 3.9 18.3 + - - +
59A TYR* 3.5 19.1 + + - +
61A ALA* 1.3 78.6 - - - +
63A GLU* 1.3 68.1 + - + +
65A TRP* 3.2 34.1 + + + +
66A LEU* 3.2 26.3 + - + +
101A PHE* 4.0 28.9 - + - -
104A ILE* 4.1 23.3 - - + -
105A ASP* 2.4 42.8 + - + -
108A LEU* 3.4 23.6 - - + +
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Residues in contact with GLU 63 (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 PRO* 5.4 1.6 - - - +
59A TYR* 3.0 54.5 + - + +
60A ARG* 4.6 12.9 - - + +
62A TRP* 1.3 82.3 - - + +
64A MET* 1.3 62.3 + - + +
65A TRP 3.5 0.2 + - - -
66A LEU* 3.6 8.6 + - + +
67A VAL* 3.4 25.6 + - - +
105A ASP* 5.8 0.9 - - - +
177A ARG* 5.6 8.2 + - - +
181A LEU* 5.4 1.2 - - - +
184A ARG* 3.7 34.0 + - - +
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Residues in contact with MET 64 (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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60A ARG* 3.9 20.4 + - - +
61A ALA* 3.6 9.7 + - - +
62A TRP 3.3 0.8 - - - -
63A GLU* 1.3 77.5 - - + +
65A TRP* 1.3 60.6 + - - +
67A VAL* 3.8 17.0 + - - +
68A LEU* 3.9 13.5 + - - +
181A LEU* 4.2 28.7 - - + -
184A ARG* 5.7 4.3 - - - +
185A LEU* 6.1 4.9 - - + -
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Residues in contact with TRP 65 (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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61A ALA 3.4 11.8 + - - +
62A TRP* 3.2 27.7 + + + +
63A GLU 3.2 0.4 - - - -
64A MET* 1.3 77.0 - - - +
66A LEU* 1.3 67.3 + - + +
67A VAL 3.2 1.8 - - - -
68A LEU* 3.2 29.1 + - + +
69A LEU* 3.4 35.1 + - + +
101A PHE* 3.4 53.6 - + + -
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Residues in contact with LEU 66 (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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62A TRP* 3.2 29.0 + - + +
63A GLU* 3.6 9.4 + - + +
64A MET 3.5 0.4 - - - -
65A TRP* 1.3 78.9 - - + +
67A VAL* 1.3 64.1 + - + +
69A LEU* 3.3 16.1 + - + +
70A VAL* 3.3 27.1 + - - +
101A PHE* 3.9 19.7 - - + +
102A PHE* 3.9 24.0 - - + -
105A ASP* 3.4 40.4 - - + +
177A ARG* 4.4 22.0 - - + +
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Residues in contact with VAL 67 (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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63A GLU 3.4 16.3 + - - +
64A MET* 3.9 15.5 - - - +
65A TRP 3.2 0.6 - - - -
66A LEU* 1.3 78.3 - - + +
68A LEU* 1.3 59.9 + - + +
70A VAL* 3.0 20.5 + - - +
71A ILE* 3.1 27.1 + - + +
177A ARG* 4.2 18.6 - - + +
178A VAL* 4.0 17.0 - - + -
181A LEU* 3.7 33.4 - - + -
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Residues in contact with LEU 68 (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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64A MET 4.1 12.8 - - - +
65A TRP* 3.2 24.0 + - + +
67A VAL* 1.3 79.4 - - + +
69A LEU* 1.3 63.9 + - + +
70A VAL 3.3 0.2 - - - -
71A ILE* 4.1 21.3 - - + +
72A TYR* 3.5 23.0 + - - +
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Residues in contact with LEU 69 (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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65A TRP* 3.4 53.3 + - + +
66A LEU* 3.3 12.2 + - + +
67A VAL 3.2 1.0 - - - -
68A LEU* 1.3 82.6 - - + +
70A VAL* 1.3 61.0 + - - +
72A TYR* 4.6 7.6 - - + +
73A SER* 3.3 24.6 + - - -
98A VAL* 4.0 28.6 - - + +
101A PHE* 4.0 22.9 - - + -
102A PHE* 3.6 23.9 - - + -
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Residues in contact with VAL 70 (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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66A LEU 3.3 14.4 - - - +
67A VAL* 3.0 8.1 + - - +
69A LEU* 1.3 78.2 - - - +
71A ILE* 1.3 61.1 + - - +
72A TYR 3.2 1.6 - - - -
73A SER* 3.5 3.8 - - - +
74A ALA* 2.9 30.7 + - + +
102A PHE* 3.6 21.5 - - + -
174A ARG* 3.3 35.0 - - + +
175A LEU* 3.7 24.2 - - + -
177A ARG* 4.2 10.1 - - + -
178A VAL* 3.7 17.5 - - + -
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Residues in contact with ILE 71 (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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67A VAL* 3.1 28.3 + - + +
68A LEU* 4.3 20.9 - - + +
70A VAL* 1.3 76.1 - - - +
72A TYR* 1.3 61.3 + - - +
74A ALA* 3.8 1.6 + - - +
75A TRP* 3.5 19.9 + - - +
178A VAL* 4.5 13.0 - - + -
701A 3PE 4.3 34.2 - - + +
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Residues in contact with TYR 72 (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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68A LEU 3.5 17.3 + - - +
69A LEU* 4.6 5.2 - - + -
70A VAL 3.2 0.4 - - - -
71A ILE* 1.3 79.9 - - - +
73A SER* 1.3 63.5 + - - +
74A ALA 3.1 0.4 - - - -
75A TRP* 3.0 20.1 + - + +
76A ILE* 3.3 58.5 + - + +
91A ILE* 4.0 15.2 - - + +
94A ILE* 3.4 39.7 - - + +
95A ASP* 5.3 1.1 - - - -
98A VAL* 4.2 22.7 - - + -
171A ARG* 5.7 0.2 - - - -
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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
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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