Contacts of the helix formed by residues 95 - 106 (chain A) in PDB entry 6A5T
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 PHE 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.4 19.5 - - + -
92A HIS* 3.1 55.9 - + + +
93A ILE 3.1 1.4 - - - -
94A GLY* 1.3 84.8 - - - +
96A ILE* 1.3 64.2 + - - +
97A PRO* 3.3 3.4 - - - -
98A LYS* 3.9 12.8 - - + +
99A ILE* 2.8 51.5 + - + +
235A MET* 4.1 22.4 - - + +
1413A PHE* 3.4 39.0 - + + -
1417A ALA* 3.6 18.4 - - + -
1211B ASN 5.1 2.0 - - - -
1212B ILE* 4.6 1.1 - - + -
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Residues in contact with ILE 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* 4.4 19.3 - - + -
92A HIS 4.1 12.0 + - - +
93A ILE* 4.0 25.5 + - + +
95A PHE* 1.3 76.1 - - - +
97A PRO* 1.3 65.2 - - + +
99A ILE* 3.8 3.8 - - - +
100A LYS* 2.8 27.7 + - - +
177A LYS* 3.5 37.5 - - + -
179A GLY 3.8 18.8 - - - +
180A MET* 3.9 19.3 - - + -
182A LEU* 4.6 17.6 - - + +
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Residues in contact with PRO 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 2.7 - - - +
94A GLY 4.7 4.7 - - - +
95A PHE* 3.5 7.6 - - - +
96A ILE* 1.3 96.8 - - + +
98A LYS* 1.3 63.1 + - + +
100A LYS* 3.1 12.9 - - + +
101A LYS* 3.0 26.9 + - - +
177A LYS* 4.7 15.5 - - + -
1414A GLU* 6.2 0.2 - - - +
-26N C 5.5 7.0 - - - +
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Residues in contact with LYS 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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94A GLY 5.4 0.7 - - - +
95A PHE* 3.4 16.0 + - + +
96A ILE 3.4 0.4 - - - -
97A PRO* 1.3 82.8 - - + +
99A ILE* 1.3 63.8 + - - +
101A LYS* 3.0 25.9 + - + +
102A VAL* 3.0 13.8 + - + +
135A PHE* 5.0 20.4 - - + +
225A PHE* 4.3 18.3 - - + -
235A MET* 4.2 15.3 - - - -
1414A GLU* 3.2 38.7 + - - +
1417A ALA* 3.6 30.9 + - + +
1418A ALA* 6.1 2.2 - - - +
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Residues in contact with ILE 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* 5.4 9.4 - - + -
92A HIS 5.6 1.1 - - - +
95A PHE* 2.8 30.3 + - + +
96A ILE* 4.0 3.6 - - - +
98A LYS* 1.3 69.8 - - - +
100A LYS* 1.3 65.6 + - - +
102A VAL* 4.3 4.5 - - - +
103A CYS* 2.9 33.6 + - - -
182A LEU* 5.3 11.2 - - + -
208A ILE* 4.8 2.9 - - + -
212A PHE* 3.9 19.3 - - + -
235A MET* 3.1 60.3 - - + +
236A ILE* 3.6 15.0 - - + -
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Residues in contact with LYS 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 ILE 2.8 14.4 + - - +
97A PRO* 3.1 13.7 - - + +
99A ILE* 1.3 77.0 - - - +
101A LYS* 1.3 66.8 + - + +
103A CYS* 3.7 1.7 - - - +
104A GLU* 2.4 52.9 + - - +
139A TRP* 4.9 6.3 - - - -
175A VAL* 3.3 39.1 - - + +
176A ARG* 4.2 7.0 - - - +
177A LYS* 4.1 22.7 - - + +
182A LEU* 4.9 10.6 - - + +
-26N C 4.8 12.2 + - - -
-25N C 4.1 20.2 + - - -
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Residues in contact with LYS 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 PRO* 3.0 18.8 + - - +
98A LYS* 3.0 22.0 + - - +
100A LYS* 1.3 80.7 - - + +
102A VAL* 1.3 64.0 + - - +
104A GLU* 2.8 23.3 + - - +
105A CYS* 3.0 13.5 + - - -
135A PHE* 3.3 34.0 - - + -
136A ASN* 5.1 7.4 + - - -
139A TRP* 3.2 46.8 - - + +
-26N C 4.1 20.8 + - - +
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Residues in contact with VAL 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 LYS* 3.0 14.8 + - + +
99A ILE* 3.3 4.7 + - - +
101A LYS* 1.3 74.6 - - - +
103A CYS* 1.3 58.9 + - - +
105A CYS* 2.8 27.4 + - - +
106A ILE* 3.4 12.7 + - + +
135A PHE* 3.7 15.0 - - + -
212A PHE* 3.8 28.9 - - + -
215A ILE* 5.8 0.9 - - + -
223A LEU* 3.9 18.4 - - + -
225A PHE* 3.6 37.0 - - + -
232A PRO* 5.3 6.3 - - + -
235A MET* 4.7 3.6 - - + -
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Residues in contact with CYS 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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99A ILE* 2.9 25.0 + - - +
100A LYS* 3.9 4.5 - - - +
102A VAL* 1.3 76.5 - - - +
104A GLU* 1.3 61.5 + - - +
106A ILE* 3.8 10.8 - - - +
108A MET* 3.7 28.0 - - + +
172A GLN* 5.2 0.3 - - - +
173A PRO* 5.9 0.5 - - - +
175A VAL* 4.4 19.3 - - + +
182A LEU* 5.9 2.7 - - + -
203A LEU* 5.2 2.9 - - + -
208A ILE* 3.8 27.1 - - - -
212A PHE* 3.5 26.2 - - - -
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Residues in contact with GLU 104 (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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100A LYS* 2.4 49.3 + - - +
101A LYS* 2.8 10.5 + - - +
103A CYS* 1.3 76.4 - - - +
105A CYS* 1.3 65.6 + - - +
106A ILE 3.5 1.9 + - - +
114A LEU* 4.1 12.1 - - - +
139A TRP* 2.5 48.5 + - + +
142A CYS 4.2 5.7 - - - +
143A LYS* 4.7 6.3 - - - +
172A GLN* 5.7 2.3 - - - +
173A PRO 6.1 1.6 - - - +
175A VAL* 3.5 25.4 + - + +
-25N C 4.7 3.5 + - - -
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Residues in contact with CYS 105 (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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101A LYS 3.0 14.3 + - - -
102A VAL* 2.8 12.1 + - - +
104A GLU* 1.3 77.3 - - - +
106A ILE* 1.3 64.6 + - + +
113A LEU* 3.3 27.4 - - + +
114A LEU* 3.2 24.4 - - - +
135A PHE* 4.2 13.5 - - - -
138A VAL* 4.6 2.7 - - - -
139A TRP* 4.2 26.2 - - - -
142A CYS* 4.1 6.8 - - - +
223A LEU* 3.8 24.9 - - + -
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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
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102A VAL* 3.4 14.1 + - + +
103A CYS* 3.8 13.9 + - - +
104A GLU 4.2 2.1 - - - +
105A CYS* 1.3 91.9 - - + +
107A CYS* 1.3 70.5 + - - +
108A MET* 5.6 0.7 - - + -
111A GLY* 3.8 15.5 - - - +
112A LYS* 3.3 13.0 - - - +
113A LEU* 3.7 21.3 - - + +
114A LEU* 4.7 2.9 - - - +
172A GLN* 3.1 13.0 - - - +
211A VAL* 4.7 2.7 - - + -
212A PHE* 4.1 19.5 - - + -
215A ILE* 3.7 30.1 - - + -
219A ASP* 5.5 3.6 - - + -
223A LEU* 4.4 14.1 - - + -
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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