Contacts of the helix formed by residues 93 - 109 (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 ILE 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASP* 4.7 9.9 - - - +
90B ALA 4.2 12.6 - - - +
92B PHE* 1.3 85.7 - - + +
94B ILE* 1.3 75.6 + - + +
96B ASN* 3.3 4.4 + - - +
97B ILE* 2.9 42.2 + - + +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.4 31.4 - - + +
90B ALA 5.2 1.8 - - - +
91B ILE* 3.2 28.8 + - + +
93B ILE* 1.3 91.1 - - + +
95B ASP* 1.3 56.9 + - - +
96B ASN 3.1 0.2 - - - -
97B ILE* 4.1 8.7 - - + +
98B VAL* 3.0 34.8 + - + +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 4.8 3.3 + - - +
76B ILE* 4.7 10.1 - - + -
80B GLN* 5.3 7.6 - - - +
91B ILE* 3.3 15.2 + - + +
92B PHE* 3.8 5.6 + - + +
93B ILE 3.4 0.2 - - - -
94B ILE* 1.3 77.9 - - - +
96B ASN* 1.3 60.8 + - - +
98B VAL* 4.7 5.6 - - - +
99B ASN* 3.4 22.1 + - - +
150B PRO* 5.2 6.2 - - + +
171B ARG* 4.4 25.3 + - - +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 3.2 50.3 + - - +
93B ILE* 3.3 5.4 + - - +
94B ILE 3.1 0.4 - - - -
95B ASP* 1.3 80.8 - - - +
97B ILE* 1.3 60.3 + - - +
98B VAL 3.3 0.9 - - - -
99B ASN* 3.7 9.7 + - - +
100B GLY* 3.1 21.1 + - - -
147B PRO* 4.6 8.3 - - - +
150B PRO* 3.4 26.6 - - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 2.9 32.0 + - + +
94B ILE* 4.1 8.7 - - + +
96B ASN* 1.3 76.3 - - - +
98B VAL* 1.3 65.9 + - + +
100B GLY* 3.1 10.5 + - - -
101B PHE* 3.1 38.7 + - + -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.0 40.8 - - + +
72B TYR* 4.2 20.0 - - + -
73B SER* 4.5 7.6 - - - -
94B ILE* 3.0 25.8 + - + +
95B ASP* 4.7 4.7 - - - +
97B ILE* 1.3 80.6 - - + +
99B ASN* 1.3 61.2 + - - +
101B PHE* 3.1 16.9 + - + +
102B PHE* 3.2 24.5 - - + -
171B ARG* 6.1 1.8 - - - +
174B ARG* 3.9 20.2 - - - +
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP 3.4 20.3 + - - +
96B ASN* 3.6 12.2 + - - +
97B ILE 3.3 0.6 - - - -
98B VAL* 1.3 80.3 - - - +
100B GLY* 1.3 57.1 + - - +
102B PHE* 4.0 4.5 + - - +
103B ALA* 3.8 16.1 + - - +
144B SER 5.1 0.2 + - - -
145B THR* 3.0 33.6 + - - +
146B ALA 4.6 0.4 + - - -
147B PRO* 3.8 26.3 - - + +
150B PRO* 5.6 2.0 - - - +
171B ARG* 5.4 10.0 - - - +
174B ARG* 3.4 24.9 + - - +
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Residues in contact with GLY 100 (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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96B ASN 3.1 10.3 + - - -
97B ILE* 3.1 8.1 + - - -
98B VAL 3.1 1.2 - - - -
99B ASN* 1.3 74.4 - - - +
101B PHE* 1.3 64.9 + - - +
102B PHE 3.2 1.8 - - - -
103B ALA* 3.2 17.4 + - - +
104B ILE* 3.3 19.0 + - - +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TRP* 4.0 18.3 - + - -
65B TRP* 3.4 39.3 - + + -
66B LEU* 3.9 14.7 - - + +
69B LEU* 4.0 18.4 - - + -
97B ILE* 3.1 40.8 + - + -
98B VAL 3.1 8.1 + - - +
100B GLY* 1.3 76.5 - - - +
102B PHE* 1.3 60.0 + - + +
103B ALA 3.4 0.2 - - - -
104B ILE* 4.1 21.9 + - + -
105B ASP* 3.9 12.5 + - - +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.9 19.1 - - + -
69B LEU* 3.6 31.4 - - + -
70B VAL* 3.6 25.1 - - + -
98B VAL* 3.2 24.1 + - + +
99B ASN* 4.4 5.6 - - - +
100B GLY 3.2 0.8 - - - -
101B PHE* 1.3 81.0 - - + +
103B ALA* 1.3 58.0 + - - +
104B ILE 3.5 0.4 - - - -
105B ASP* 4.0 6.9 + - + +
106B ILE* 3.3 24.4 + - - +
145B THR* 3.8 15.7 + - - +
174B ARG* 3.7 44.6 - - + +
177B ARG* 3.8 32.3 + - - -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN 3.8 8.5 + - - +
100B GLY* 3.2 12.3 + - - +
102B PHE* 1.3 77.4 - - - +
104B ILE* 1.3 64.3 + - - +
105B ASP 3.3 0.4 - - - -
106B ILE* 3.6 13.2 + - - +
107B ILE* 3.7 14.2 + - - +
145B THR* 3.8 19.7 - - + -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TRP* 4.1 17.9 - - + -
100B GLY 3.3 15.7 + - - +
101B PHE* 4.1 30.3 - - + +
102B PHE 3.5 0.2 - - - -
103B ALA* 1.3 79.5 - - + +
105B ASP* 1.3 56.8 + - - +
107B ILE* 3.0 13.2 + - + +
108B LEU* 2.9 29.4 + - + +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 5.0 2.5 + - - -
62B TRP* 2.4 39.1 + - + -
63B GLU* 5.8 1.1 - - - +
66B LEU* 3.4 22.5 - - + +
101B PHE 3.9 7.2 + - - +
102B PHE* 4.0 6.7 + - - +
103B ALA 3.3 0.6 - - - -
104B ILE* 1.3 76.3 - - - +
106B ILE* 1.3 64.7 + - - +
107B ILE 3.3 0.2 - - - -
108B LEU* 3.8 10.2 - - - +
109B THR* 3.2 35.8 + - - +
133B TYR* 4.4 1.4 + - - -
177B ARG* 3.5 26.1 + - - +
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE 3.3 14.4 - - - +
103B ALA* 3.6 8.0 + - - +
104B ILE 3.2 0.6 - - - -
105B ASP* 1.3 80.4 - - - +
107B ILE* 1.3 65.0 + - + +
109B THR* 3.8 6.6 + - - -
110B PHE* 3.4 19.0 - - + -
133B TYR* 3.9 14.0 - - - +
138B PHE* 3.6 33.2 - - + -
141B ASP* 3.3 29.6 - - + +
142B VAL* 4.0 15.3 - - + -
145B THR* 3.4 22.7 - - + +
177B ARG* 6.0 3.1 - - - +
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Residues in contact with ILE 107 (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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103B ALA 3.7 10.3 + - - +
104B ILE* 3.0 12.2 + - + +
106B ILE* 1.3 82.0 - - + +
108B LEU* 1.3 64.6 + - - +
110B PHE* 3.2 26.3 + - + +
111B PHE* 3.6 16.5 - - + -
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Residues in contact with LEU 108 (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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52B ILE* 5.0 15.9 - - + -
59B TYR* 4.1 18.2 - - + -
62B TRP* 3.4 42.8 - - + +
104B ILE* 2.9 20.7 + - + +
105B ASP* 3.8 7.6 + - - +
106B ILE 3.4 0.4 - - - -
107B ILE* 1.3 79.1 - - - +
109B THR* 1.3 58.5 + - + +
110B PHE 3.1 0.2 - - - -
111B PHE* 3.1 31.2 + - + +
112B VAL* 4.3 1.9 - - - +
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Residues in contact with THR 109 (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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59B TYR* 3.8 20.2 - - - +
105B ASP* 3.2 33.8 + - - +
106B ILE 3.8 0.3 + - - -
107B ILE 3.3 1.0 - - - -
108B LEU* 1.3 76.4 - - + +
110B PHE* 1.3 57.3 + - - +
111B PHE 3.3 4.0 - - - -
112B VAL* 3.8 21.1 - - + +
129B ILE* 4.4 3.1 - - - +
133B TYR* 3.1 53.0 - - + +
177B ARG* 5.6 2.2 - - - +
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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