Contacts of the helix formed by residues 110 - 122 (chain B) in PDB entry 3C07
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 TYR 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B MSE 3.5 26.2 - - + +
33B GLN* 4.0 29.2 - - - +
70B PHE* 3.8 27.6 - + + -
74B ILE* 4.1 21.9 - - + +
77B GLU* 4.6 13.1 + - - -
106B ILE* 3.5 24.7 - - + -
107B ALA* 2.6 18.9 + - + +
109B PRO* 1.3 84.5 - - + +
111B HIS* 1.3 58.7 + - - +
112B GLU 3.5 1.3 - - - -
113B PHE* 3.4 17.4 + + + +
114B ALA* 2.8 29.0 + - + +
180B TRP* 4.4 2.9 - - + -
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Residues in contact with HIS 111 (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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107B ALA 3.6 0.4 + - - -
108B THR* 3.2 16.6 + - - +
109B PRO 3.3 2.2 + - - -
110B TYR* 1.3 77.2 - - - +
112B GLU* 1.3 67.0 + - + +
114B ALA* 3.1 4.0 + - - +
115B VAL* 2.9 37.6 + - + +
180B TRP* 2.8 63.9 + - + -
181B ILE* 3.5 19.4 + - - -
183B ASP 4.3 1.9 + - - -
188B ARG* 3.3 47.8 + - - +
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Residues in contact with GLU 112 (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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109B PRO 5.2 6.1 - - - +
111B HIS* 1.3 82.4 - - + +
113B PHE* 1.3 65.3 + - - +
115B VAL* 3.3 10.1 + - - +
116B GLN* 3.1 30.9 + - + +
188B ARG* 5.4 2.4 + - - -
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Residues in contact with PHE 113 (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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32B PHE* 3.6 55.4 - + - -
33B GLN* 4.4 23.6 + - + +
37B TYR* 4.4 7.2 - - + -
67B ILE* 4.4 4.7 - - + -
70B PHE* 4.3 27.8 - + - -
110B TYR* 3.4 19.6 + + + +
111B HIS 3.3 0.6 - - - -
112B GLU* 1.3 76.0 - - - +
114B ALA* 1.3 61.7 + - + +
115B VAL 3.0 0.3 + - - -
116B GLN* 3.1 11.4 + - + +
117B PHE* 2.6 85.3 + + + +
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Residues in contact with ALA 114 (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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110B TYR* 2.8 19.4 + - + +
111B HIS 3.1 7.6 + - - +
113B PHE* 1.3 80.2 - - + +
115B VAL* 1.3 58.2 + - - +
117B PHE* 3.6 6.2 - - - -
118B PHE* 2.8 31.9 + - - +
180B TRP* 4.0 16.4 - - + -
181B ILE* 3.8 26.0 - - + +
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Residues in contact with VAL 115 (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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111B HIS* 2.9 45.5 + - + +
112B GLU* 3.8 8.1 - - - +
113B PHE 3.1 0.4 - - - -
114B ALA* 1.3 73.5 - - - +
116B GLN* 1.3 67.9 + - - +
118B PHE* 3.3 15.9 + - - +
119B LYS* 4.5 2.4 + - - +
181B ILE* 3.9 22.2 - - + +
182B PHE* 5.3 9.2 - - + -
184B ARG* 6.2 1.6 - - - +
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Residues in contact with GLN 116 (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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32B PHE 3.8 10.3 + - - -
33B GLN 3.6 21.6 + - - -
34B GLU 5.4 0.2 - - - -
35B ARG 4.4 3.4 - - - +
36B GLY* 3.4 23.9 + - - +
37B TYR 5.3 0.9 - - - +
112B GLU* 3.1 19.4 + - + +
113B PHE* 3.7 17.3 - - + +
115B VAL* 1.3 75.5 - - - +
117B PHE* 1.3 58.3 + - - +
118B PHE 2.8 7.4 + - - -
119B LYS* 2.9 34.1 - - - +
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Residues in contact with PHE 117 (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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37B TYR* 3.7 35.4 - + + +
67B ILE* 3.6 42.2 - - + -
70B PHE* 5.9 0.2 - + - -
71B TYR* 3.3 15.5 - + - -
113B PHE* 2.6 58.8 + + + +
114B ALA* 4.1 4.9 - - - +
116B GLN* 1.3 72.1 - - - +
118B PHE* 1.3 65.9 + - - +
119B LYS 3.2 0.4 - - - -
120B ASN* 3.2 21.6 + - + +
121B ALA* 3.3 27.2 + - + -
128B LEU* 3.8 14.4 - - + -
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Residues in contact with PHE 118 (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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118A PHE* 4.3 8.7 - + - -
119A LYS* 4.0 21.3 - - + -
122A ALA* 4.4 3.1 - - + -
114B ALA 2.8 18.4 + - - +
115B VAL 3.5 9.6 - - - +
116B GLN 2.8 4.2 + - - -
117B PHE* 1.3 79.8 - - - +
119B LYS* 1.3 59.3 + - + +
121B ALA* 3.1 5.4 + - + -
122B ALA* 3.0 57.0 + - + +
178B LEU* 3.4 34.5 - - + -
181B ILE* 3.6 28.5 - - + -
182B PHE* 3.6 29.2 - + + -
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Residues in contact with LYS 119 (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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39A ARG* 6.3 0.9 - - - +
119A LYS* 3.3 50.7 - - + +
38B ASP* 2.9 28.3 + - - -
115B VAL 4.5 2.0 + - - +
116B GLN* 2.9 36.3 - - - +
117B PHE 3.2 1.0 - - - -
118B PHE* 1.3 79.0 - - + +
120B ASN* 1.3 70.3 + - - +
122B ALA 4.0 3.4 + - - -
123B ASP* 4.1 7.8 + - - +
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Residues in contact with ASN 120 (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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37B TYR* 3.5 33.0 - - + +
38B ASP* 3.1 29.6 + - - +
117B PHE* 3.2 24.5 + - + +
119B LYS* 1.3 94.9 - - - +
121B ALA* 1.3 60.0 + - - +
122B ALA 3.1 6.0 + - - -
123B ASP* 3.5 18.6 - - - +
126B SER* 3.9 10.9 + - - -
128B LEU* 4.2 7.2 - - + +
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Residues in contact with ALA 121 (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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182A PHE* 5.7 0.2 - - - -
71B TYR* 3.7 11.9 - - - +
117B PHE* 3.3 36.0 + - + +
118B PHE* 3.1 8.9 + - + +
120B ASN* 1.3 77.6 - - - +
122B ALA* 1.3 58.0 + - - +
123B ASP 3.3 2.5 + - - -
128B LEU* 3.7 12.8 - - + +
129B SER* 3.2 26.9 + - - -
130B PRO* 4.1 7.9 - - + +
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Residues in contact with ALA 122 (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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115A VAL 4.6 1.2 - - - +
118A PHE* 3.6 22.0 - - + -
119A LYS* 4.0 18.0 + - + -
182A PHE* 4.3 4.8 - - - -
118B PHE* 3.0 48.7 + - + +
119B LYS 4.5 1.6 - - - +
120B ASN 3.1 0.6 - - - -
121B ALA* 1.3 76.9 - - - +
123B ASP* 1.3 52.6 + - - +
124B PRO* 2.7 24.0 - - - +
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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