Contacts of the helix formed by residues 95 - 103 (chain A) in PDB entry 6CNB
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.7 20.4 - - + +
92A HIS* 3.3 28.7 + + + +
94A GLY* 1.3 74.5 - - - +
96A PHE* 1.3 52.2 + - - +
97A LYS 3.4 1.6 - - - -
98A ALA* 2.9 13.4 + - + +
99A THR* 2.6 41.4 + - - +
256A TYR* 3.4 45.5 - + + +
1397A PHE* 3.3 41.7 - + + -
1400A ALA* 4.4 6.0 - - + +
1401A PHE* 4.7 13.5 - - + -
1136B ASN* 2.4 35.5 + - + -
1137B ILE* 3.9 7.8 - - - +
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Residues in contact with PHE 96 (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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91A PHE* 3.2 27.6 - + - -
92A HIS 3.2 17.5 + - - +
93A ILE* 3.4 28.9 - - + +
94A GLY 3.1 2.8 - - - -
95A TYR* 1.3 74.2 - - - +
97A LYS* 1.3 73.4 + - + +
99A THR* 2.5 32.5 + - - -
100A ILE* 2.9 21.8 + - + +
166A LYS* 3.5 42.8 - - + -
175A ALA 3.6 21.1 - - - -
176A LEU* 4.2 7.4 - - + -
178A ILE* 3.6 29.2 - - + -
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Residues in contact with LYS 97 (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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93A ILE 4.9 0.2 + - - -
94A GLY 4.8 3.1 + - - +
95A TYR 3.4 0.6 - - - -
96A PHE* 1.3 91.4 - - + +
98A ALA* 1.3 60.8 + - - +
100A ILE* 3.4 17.2 + - + +
101A GLN* 3.5 15.5 + - - +
166A LYS* 6.0 8.3 - - + +
1394A ASP* 5.8 1.4 + - - -
18Y T 6.4 0.6 - - - -
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Residues in contact with ALA 98 (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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95A TYR* 2.9 17.2 + - + +
97A LYS* 1.3 74.9 - - - +
99A THR* 1.3 55.4 + - - +
100A ILE 3.1 1.1 - - - -
101A GLN* 2.7 32.6 + - - +
102A ILE* 2.9 15.5 + - - +
1398A ASP* 5.4 6.7 - - - +
1401A PHE* 3.7 42.7 - - + -
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Residues in contact with THR 99 (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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91A PHE* 3.5 32.8 - - + -
92A HIS* 5.2 1.7 + - - +
95A TYR* 2.6 23.0 + - - +
96A PHE* 2.5 19.0 + - - -
98A ALA* 1.3 72.1 - - - +
100A ILE* 1.3 57.4 + - + -
102A ILE* 3.4 8.6 - - - +
103A LEU* 2.9 41.4 + - + +
231A PHE* 3.8 26.5 - - + -
256A TYR* 4.6 11.1 + - - +
257A ILE* 4.8 5.6 - - + +
1401A PHE* 5.2 0.2 - - - -
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Residues in contact with ILE 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 PHE* 2.9 32.5 + - + +
97A LYS* 3.6 12.8 - - + +
98A ALA 3.1 0.6 - - - -
99A THR* 1.3 81.9 - - + +
101A GLN* 1.3 52.0 + - - +
103A LEU* 4.7 3.4 - - + -
104A GLN* 2.4 49.0 + - - +
164A VAL* 4.2 23.1 - - + +
166A LYS* 4.9 13.5 - - + -
178A ILE* 3.7 34.5 - - + -
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Residues in contact with GLN 101 (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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97A LYS* 3.8 13.5 - - - +
98A ALA* 2.7 23.2 + - - +
100A ILE* 1.3 71.3 - - + +
102A ILE* 1.3 59.7 + - - +
103A LEU 3.0 1.1 - - - -
104A GLN* 2.6 25.6 + - + +
105A GLY* 2.8 12.5 + - - -
138A MET* 5.9 2.0 - - - +
145A LEU* 3.6 28.4 - - + +
242A LEU* 5.2 2.8 - - - +
1401A PHE* 4.6 3.7 - - + -
1402A TYR* 2.4 32.5 + - - -
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Residues in contact with ILE 102 (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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98A ALA 2.9 7.7 + - - +
99A THR* 3.3 27.1 - - + +
101A GLN* 1.3 72.8 - - - +
103A LEU* 1.3 60.5 + - - +
105A GLY 3.7 4.3 + - - -
106A ILE* 3.2 22.6 - - + +
231A PHE* 4.0 25.1 - - + -
234A ILE* 6.5 0.9 - - + -
242A LEU* 2.4 54.3 - - + +
244A ILE* 4.9 5.2 - - + -
253A PRO* 4.1 32.3 - - + -
256A TYR* 4.9 4.3 - - + -
1401A PHE* 4.4 16.9 - - + -
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Residues in contact with LEU 103 (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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91A PHE* 6.1 1.3 - - + -
99A THR* 2.9 24.4 + - + +
100A ILE* 4.7 5.2 - - + +
102A ILE* 1.3 73.7 - - - +
104A GLN* 1.3 65.8 + - - +
105A GLY 3.1 2.3 + - - -
106A ILE* 3.5 14.9 - - + +
108A LYS* 3.1 39.9 + - + +
164A VAL* 4.1 22.7 - - + -
178A ILE* 4.5 10.5 - - + -
180A HIS* 5.4 0.2 - - + -
222A LEU* 3.5 26.2 - - + -
227A THR* 3.3 28.0 - - - +
230A LEU* 5.2 5.2 - - + -
231A PHE* 4.4 11.9 - - + -
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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