Contacts of the helix formed by residues 93 - 109 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASP* 4.7 9.6 - - - +
90D ALA 4.2 12.1 - - - +
92D PHE* 1.3 85.5 - - + +
94D ILE* 1.3 73.5 + - + +
96D ASN* 3.3 3.8 + - - +
97D ILE* 2.9 43.8 + - + +
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 3.4 30.5 - - + +
90D ALA 5.2 1.6 - - - +
91D ILE* 3.2 29.5 + - + +
93D ILE* 1.3 90.7 - - + +
95D ASP* 1.3 57.1 + - - +
96D ASN 3.1 0.2 - - - -
97D ILE* 4.1 8.7 - - + +
98D VAL* 3.0 34.3 + - + +
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Residues in contact with ASP 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 4.8 3.3 + - - -
76D ILE* 4.7 9.6 - - + -
80D GLN* 5.3 9.0 - - - +
91D ILE* 3.3 15.2 + - + +
92D PHE* 4.4 5.6 - - + +
93D ILE 3.4 0.4 - - - -
94D ILE* 1.3 76.9 - - - +
96D ASN* 1.3 62.1 + - - +
98D VAL* 4.7 5.0 - - - +
99D ASN* 3.4 22.1 + - - +
150D PRO* 5.2 6.1 - - + +
171D ARG* 4.4 25.2 + - - +
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Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D PHE* 3.2 49.0 + - - +
93D ILE* 3.3 6.4 + - - +
94D ILE 3.1 0.2 - - - -
95D ASP* 1.3 81.1 - - - +
97D ILE* 1.3 60.6 + - - +
98D VAL 3.3 0.4 - - - -
99D ASN* 3.7 10.5 + - - +
100D GLY* 3.1 20.8 + - - -
147D PRO* 4.6 8.3 - - - +
150D PRO* 3.4 26.7 - - - +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 2.9 30.5 + - + +
94D ILE* 4.1 9.6 - - + +
96D ASN* 1.3 76.8 - - - +
98D VAL* 1.3 65.8 + - + +
100D GLY* 3.1 11.5 + - - -
101D PHE* 3.1 38.2 + - + -
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 4.0 41.1 - - + +
72D TYR* 4.2 19.3 - - + -
73D SER* 4.5 7.0 - - - -
94D ILE* 3.0 26.1 + - + +
95D ASP* 4.7 4.7 - - - +
97D ILE* 1.3 81.1 - - + +
99D ASN* 1.3 61.4 + - - +
101D PHE* 3.1 16.3 + - - +
102D PHE* 3.2 25.0 - - + -
171D ARG* 6.1 2.2 - - - +
174D ARG* 3.9 20.6 - - - +
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Residues in contact with ASN 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ASP 3.4 20.6 + - - +
96D ASN* 3.6 11.7 + - - +
97D ILE 3.3 0.4 - - - -
98D VAL* 1.3 79.9 - - + +
100D GLY* 1.3 58.6 + - - +
102D PHE* 4.0 4.3 + - - +
103D ALA* 3.8 15.6 + - - +
144D SER 5.1 0.2 + - - -
145D THR* 3.0 34.0 + - - +
146D ALA 4.8 0.2 + - - -
147D PRO* 3.8 25.9 - - + +
150D PRO* 5.6 2.2 - - - +
171D ARG* 5.4 10.6 - - - +
174D ARG* 3.4 25.0 + - - +
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Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASN 3.1 10.5 + - - -
97D ILE* 3.1 8.1 + - - -
98D VAL 3.1 0.8 - - - -
99D ASN* 1.3 74.7 - - - +
101D PHE* 1.3 65.9 + - - +
102D PHE 3.2 2.0 - - - -
103D ALA* 3.2 16.1 + - - +
104D ILE* 3.3 19.5 + - - +
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Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D TRP* 4.0 18.2 - + - -
65D TRP* 3.4 39.7 - + + -
66D LEU* 3.9 14.6 - - + +
69D LEU* 4.0 17.9 - - + -
97D ILE* 3.1 42.5 + - + -
98D VAL* 3.1 8.3 + - + +
100D GLY* 1.3 77.1 - - - +
102D PHE* 1.3 60.3 + - - +
103D ALA 3.4 0.2 - - - -
104D ILE* 4.1 23.5 + - + -
105D ASP* 3.9 11.8 + - - +
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Residues in contact with PHE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU* 3.9 19.7 - - + -
69D LEU* 3.6 31.2 - - + -
70D VAL* 3.6 26.0 - - + -
98D VAL* 3.2 24.6 + - + +
99D ASN 4.0 5.1 + - - +
100D GLY 3.2 0.6 - - - -
101D PHE* 1.3 81.6 - - + +
103D ALA* 1.3 57.7 + - - +
104D ILE 3.5 0.4 - - - -
105D ASP* 4.0 7.6 - - + +
106D ILE* 3.3 24.1 + - - +
145D THR* 3.7 15.3 + - - +
174D ARG* 3.7 45.1 - - + +
177D ARG* 3.8 32.9 + - - -
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN 3.8 7.2 + - - +
100D GLY* 3.2 12.7 + - - +
102D PHE* 1.3 78.1 - - - +
104D ILE* 1.3 64.4 + - - +
105D ASP 3.3 0.4 - - - -
106D ILE* 3.6 13.7 + - + +
107D ILE* 3.7 14.2 + - - +
145D THR* 3.8 19.5 - - + -
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D TRP* 4.1 19.7 - - + -
100D GLY 3.3 14.7 + - - +
101D PHE* 4.1 31.4 - - + +
102D PHE 3.5 0.2 - - - -
103D ALA* 1.3 77.8 - - + +
105D ASP* 1.3 56.5 + - - +
107D ILE* 3.0 12.9 + - + +
108D LEU* 2.9 29.5 + - + +
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Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 5.0 2.9 + - - -
62D TRP* 2.4 39.2 + - + -
63D GLU* 5.8 1.3 - - - +
66D LEU* 3.4 22.1 - - + +
101D PHE 3.9 6.9 + - - +
102D PHE* 4.0 7.1 + - - +
103D ALA 3.3 0.8 - - - -
104D ILE* 1.3 75.3 - - - +
106D ILE* 1.3 66.0 + - - +
107D ILE 3.3 0.2 - - - -
108D LEU* 3.8 9.5 - - - +
109D THR* 3.2 36.6 + - - +
133D TYR* 4.5 1.4 + - - -
177D ARG* 3.5 26.8 + - - +
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PHE 3.3 14.1 - - - +
103D ALA* 3.8 7.6 - - - +
104D ILE 3.2 0.8 - - - -
105D ASP* 1.3 80.6 - - - +
107D ILE* 1.3 64.1 + - + +
109D THR* 3.8 6.4 + - - -
110D PHE* 3.4 19.0 - - + -
133D TYR* 3.9 14.0 - - - +
138D PHE* 3.6 32.3 - - + -
141D ASP* 3.3 29.2 - - + +
142D VAL* 4.0 15.9 - - + -
145D THR* 3.4 23.1 - - + +
177D ARG* 6.0 2.9 - - - +
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ALA 3.7 10.5 + - - +
104D ILE* 3.0 13.1 + - + +
106D ILE* 1.3 81.9 - - + +
108D LEU* 1.3 65.3 + - - +
110D PHE* 3.2 26.1 + - + +
111D PHE* 3.6 15.7 - - + -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ILE* 5.0 16.4 - - + -
59D TYR* 4.1 18.4 - - + -
62D TRP* 3.4 42.8 - - + +
104D ILE* 2.9 20.5 + - + +
105D ASP* 4.0 7.9 - - - +
106D ILE 3.4 0.4 - - - -
107D ILE* 1.3 80.6 - - + +
109D THR* 1.3 58.7 + - + +
110D PHE 3.1 0.4 - - - -
111D PHE* 3.1 30.7 + - + +
112D VAL* 4.3 2.2 - - + +
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Residues in contact with THR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 3.8 19.7 - - - +
105D ASP* 3.2 34.6 + - - +
106D ILE 3.8 0.7 + - - -
107D ILE 3.3 0.6 - - - -
108D LEU* 1.3 76.0 - - + +
110D PHE* 1.3 56.0 + - - +
111D PHE 3.3 4.3 - - - -
112D VAL* 3.8 22.2 - - + +
129D ILE* 4.4 2.8 - - - +
133D TYR* 3.1 51.5 - - + +
177D 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
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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