Contacts of the helix formed by residues 93 - 109 (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 ILE 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASP* 4.7 10.1 - - - +
90A ALA 4.2 11.0 - - - +
92A PHE* 1.3 84.2 - - + +
94A ILE* 1.3 74.3 + - + +
96A ASN* 3.7 3.8 - - - +
97A ILE* 2.9 44.2 + - + +
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Residues in contact with ILE 94 (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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72A TYR* 3.4 31.2 - - + +
90A ALA 5.2 1.6 - - - +
91A ILE* 3.2 29.5 + - + +
93A ILE* 1.3 91.4 - - + +
95A ASP* 1.3 56.3 + - - +
96A ASN 3.1 0.2 - - - -
97A ILE* 4.1 8.7 - - + +
98A VAL* 3.0 35.2 + - + +
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 4.8 2.8 + - - -
76A ILE* 4.7 10.3 - - + -
80A GLN* 5.3 8.5 - - - +
91A ILE* 3.3 14.3 + - + +
92A PHE* 3.8 5.8 + - + +
93A ILE 3.4 0.2 - - - -
94A ILE* 1.3 77.6 - - - +
96A ASN* 1.3 61.9 + - - +
98A VAL* 4.7 5.5 - - - +
99A ASN* 3.4 21.6 + - - +
150A PRO* 5.2 6.3 - - + +
171A ARG* 4.4 25.3 + - - +
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Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.2 49.8 + - - +
93A ILE* 3.3 6.3 + - - +
94A ILE 3.1 0.6 - - - -
95A ASP* 1.3 80.2 - - - +
97A ILE* 1.3 60.2 + - - +
98A VAL 3.3 0.7 - - - -
99A ASN* 3.7 9.7 + - - +
100A GLY* 3.1 21.1 + - - -
147A PRO* 4.6 7.8 - - - +
150A PRO* 3.4 26.5 - - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 2.9 31.3 + - + +
94A ILE* 4.1 9.0 - - + +
96A ASN* 1.3 77.3 - - - +
98A VAL* 1.3 65.1 + - + +
100A GLY* 3.1 11.1 + - - -
101A PHE* 3.1 37.8 + - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.0 41.1 - - + +
72A TYR* 4.2 18.4 - - + -
73A SER* 4.5 7.4 - - - -
94A ILE* 3.0 26.3 + - + +
95A ASP* 4.7 4.7 - - - +
97A ILE* 1.3 80.0 - - + +
99A ASN* 1.3 62.1 + - - +
100A GLY 3.1 0.2 - - - -
101A PHE* 3.1 16.8 + - + +
102A PHE* 3.2 23.9 - - + -
171A ARG* 6.1 1.8 - - - +
174A ARG* 3.9 20.9 - - - +
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP 3.4 20.5 + - - +
96A ASN* 3.6 12.7 + - - +
97A ILE 3.3 0.4 - - - -
98A VAL* 1.3 79.1 - - + +
100A GLY* 1.3 58.5 + - - +
102A PHE* 4.0 4.1 + - - +
103A ALA* 3.8 16.1 + - - +
144A SER 5.1 0.4 + - - -
145A THR* 3.0 33.9 + - - +
146A ALA 4.6 0.2 - - - -
147A PRO* 3.8 26.3 - - + +
150A PRO* 5.6 2.2 - - - +
171A ARG* 5.4 10.7 - - - +
174A ARG* 3.4 24.5 + - - +
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Residues in contact with GLY 100 (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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96A ASN 3.1 10.1 + - - -
97A ILE* 3.1 8.3 + - - -
98A VAL 3.1 0.8 - - - -
99A ASN* 1.3 75.3 - - - +
101A PHE* 1.3 66.0 + - - +
102A PHE 3.2 2.2 - - - -
103A ALA* 3.2 16.3 + - - +
104A ILE* 3.3 19.4 + - - +
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 4.0 19.0 - + + -
65A TRP* 3.4 37.0 - + + -
66A LEU* 3.9 14.9 - - + +
69A LEU* 4.0 18.4 - - + -
97A ILE* 3.1 41.2 + - + -
98A VAL* 3.1 8.3 + - + +
100A GLY* 1.3 77.1 - - - +
102A PHE* 1.3 60.5 + - - +
103A ALA 3.4 0.4 - - - -
104A ILE* 4.1 23.0 + - + +
105A ASP* 3.9 12.3 + - - +
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.9 20.2 - - + -
69A LEU* 3.6 31.4 - - + -
70A VAL* 3.6 25.8 - - + -
98A VAL* 3.2 23.7 + - + +
99A ASN* 4.0 5.6 + - - +
100A GLY 3.2 0.6 - - - -
101A PHE* 1.3 79.1 - - + +
103A ALA* 1.3 59.6 + - - +
104A ILE 3.5 0.7 - - - -
105A ASP* 4.0 7.0 + - + +
106A ILE* 3.3 23.6 + - - +
145A THR* 3.7 15.6 + - - +
174A ARG* 3.7 44.0 - - + +
177A ARG* 3.8 33.9 + - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN 3.8 8.0 + - - +
100A GLY* 3.2 13.1 + - - +
102A PHE* 1.3 77.6 - - - +
104A ILE* 1.3 63.5 + - + +
105A ASP 3.3 0.4 - - - -
106A ILE* 3.6 13.6 + - - +
107A ILE* 3.7 14.4 + - - +
145A THR* 3.8 20.4 - - + -
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 4.1 20.0 - - + -
100A GLY 3.3 16.2 + - - +
101A PHE* 4.1 29.4 - - + +
102A PHE 3.5 0.2 - - - -
103A ALA* 1.3 78.7 - - + +
105A ASP* 1.3 57.3 + - - +
107A ILE* 3.0 12.6 + - + +
108A LEU* 2.9 30.2 + - + +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 5.0 3.0 + - - -
62A TRP* 2.4 38.7 + - + -
63A GLU* 5.8 1.1 - - - +
66A LEU* 3.4 23.5 - - + +
101A PHE 3.9 7.7 + - - +
102A PHE* 4.0 6.9 + - - +
103A ALA 3.3 0.4 - - - -
104A ILE* 1.3 75.5 - - - +
106A ILE* 1.3 64.6 + - - +
108A LEU* 3.8 10.0 - - - +
109A THR* 3.2 36.7 + - - +
133A TYR* 4.5 1.8 + - - -
177A ARG* 3.5 26.0 + - - +
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE 3.3 15.0 + - - +
103A ALA* 3.6 9.1 + - - +
104A ILE 3.2 0.8 - - - -
105A ASP* 1.3 79.0 - - - +
107A ILE* 1.3 64.3 + - + +
109A THR* 3.8 6.4 + - - -
110A PHE* 3.4 18.9 - - + -
133A TYR* 3.9 13.9 - - - +
138A PHE* 3.6 32.5 - - + -
141A ASP* 3.3 29.2 - - + +
142A VAL* 4.0 16.2 - - + -
145A THR* 3.4 23.1 - - + +
177A ARG* 6.0 2.9 - - - +
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Residues in contact with ILE 107 (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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103A ALA 3.7 10.5 + - - +
104A ILE* 3.0 12.2 + - + +
106A ILE* 1.3 82.8 - - + +
108A LEU* 1.3 65.7 + - - +
110A PHE* 3.2 22.9 + - + +
111A PHE* 3.6 19.9 - - + -
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Residues in contact with LEU 108 (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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52A ILE* 5.0 15.9 - - + -
59A TYR* 4.1 18.2 - - + -
62A TRP* 3.4 42.8 - - + +
104A ILE* 2.9 21.1 + - + +
105A ASP* 3.8 8.9 + - - +
106A ILE 3.4 0.4 - - - -
107A ILE* 1.3 79.3 - - - +
109A THR* 1.3 58.1 + - - +
111A PHE* 3.1 31.4 + - + +
112A VAL* 4.3 1.6 - - - +
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Residues in contact with THR 109 (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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59A TYR* 3.8 19.3 - - - +
105A ASP* 3.2 34.8 + - - +
106A ILE 3.8 0.3 + - - -
107A ILE 3.3 0.8 - - - -
108A LEU* 1.3 76.0 - - + +
110A PHE* 1.3 57.8 + - - +
111A PHE 3.3 3.6 - - - -
112A VAL* 3.8 22.2 - - + +
129A ILE* 4.4 3.3 - - - +
133A TYR* 3.1 52.3 - - + +
177A ARG* 5.6 2.7 - - - +
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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