Contacts of the helix formed by residues 94 - 106 (chain A) in PDB entry 6E8Y
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 PRO 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY* 6.1 5.6 - - - +
92A VAL 4.7 0.7 - - - +
93A VAL* 1.3 92.8 - - + +
95A HIS* 1.3 67.4 + - - +
96A GLN* 4.2 10.1 - - + +
97A PHE* 2.9 45.0 + - + +
98A ILE 3.6 6.6 + - - -
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Residues in contact with HIS 95 (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 VAL 3.4 2.6 + - - -
94A PRO* 1.3 71.7 - - - +
96A GLN* 1.3 61.8 + - - +
97A PHE 3.1 1.4 + - - -
98A ILE* 3.3 24.9 - - + +
99A GLY 4.6 0.3 + - - -
119A ILE* 3.9 19.3 - - + +
120A LYS 5.4 2.9 - - - +
121A GLY* 5.7 1.1 - - - -
122A VAL 3.3 24.9 + - - -
123A ASP* 2.5 33.9 + - - -
132A ILE* 3.6 25.7 - - + +
298A GLN* 6.5 1.1 - - - -
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Residues in contact with GLN 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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94A PRO* 2.9 8.4 + - + +
95A HIS* 1.3 78.9 - - - +
97A PHE* 1.3 103.3 + - + +
99A GLY 4.9 1.5 + - - -
100A LYS* 5.4 1.9 + - - +
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Residues in contact with PHE 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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39A TRP* 5.9 4.0 - + + -
93A VAL* 4.6 2.5 - - + -
94A PRO* 2.9 41.5 + - + +
96A GLN* 1.3 113.5 - - + +
98A ILE* 1.3 64.7 + - - +
99A GLY 3.1 3.6 - - - -
100A LYS* 3.1 12.0 + - + +
101A ILE* 3.0 37.4 + - + +
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Residues in contact with ILE 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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91A PHE* 3.7 21.3 - - + -
93A VAL* 3.9 11.9 - - + -
94A PRO 3.6 3.2 + - - +
95A HIS* 3.3 34.2 + - + +
97A PHE* 1.3 76.6 - - - +
99A GLY* 1.3 67.4 + - - +
101A ILE* 3.4 6.0 + - + +
102A CYS* 2.9 27.3 + - - -
119A ILE* 3.7 23.3 - - + -
123A ASP* 5.1 1.6 - - - +
132A ILE* 4.3 8.5 - - + -
135A VAL* 5.1 8.3 - - + -
136A ILE* 3.5 41.5 - - + -
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Residues in contact with GLY 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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95A HIS 4.6 1.0 + - - -
96A GLN 4.9 1.8 + - - -
97A PHE 3.1 1.4 + - - -
98A ILE* 1.3 86.4 - - - +
100A LYS* 1.3 55.4 + - - +
102A CYS* 3.3 1.6 + - - +
103A ASP* 3.0 34.9 + - - -
135A VAL* 5.4 3.6 - - - -
139A ARG* 3.5 22.8 + - - -
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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 GLN 5.4 1.5 + - - +
97A PHE* 3.1 14.8 + - + +
99A GLY* 1.3 72.6 - - - +
101A ILE* 1.3 67.0 + - + +
103A ASP* 3.2 10.2 + - - +
104A GLN* 3.1 29.4 + - + +
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Residues in contact with ILE 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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9A VAL* 3.7 23.6 - - + -
39A TRP* 3.5 40.2 - - + -
79A VAL* 4.3 7.2 - - + -
91A PHE* 4.7 6.7 - - + -
93A VAL* 3.5 32.5 - - + -
97A PHE* 3.0 23.9 + - + +
98A ILE* 3.8 7.6 - - + +
100A LYS* 1.3 77.7 - - + +
102A CYS* 1.3 65.4 + - - +
104A GLN* 3.1 11.6 + - - +
105A LEU* 3.0 36.0 + - + +
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Residues in contact with CYS 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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91A PHE* 4.7 2.9 - - - -
98A ILE* 2.9 28.6 + - - +
99A GLY* 3.8 4.7 - - - +
101A ILE* 1.3 76.7 - - - +
103A ASP* 1.3 58.7 + - - +
105A LEU* 4.5 1.1 - - - -
106A LYS* 2.9 30.9 + - - +
135A VAL* 5.4 2.2 - - + -
136A ILE* 3.7 45.8 - - - -
139A ARG* 4.1 23.3 - - + +
140A LEU* 3.4 20.2 - - + +
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Residues in contact with ASP 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 GLY 3.0 20.8 + - - +
100A LYS* 3.6 11.2 - - - +
101A ILE 3.2 0.6 - - - -
102A CYS* 1.3 77.5 - - - +
104A GLN* 1.3 61.8 + - + +
106A LYS* 3.9 18.3 + - - +
139A ARG* 3.3 27.0 + - - -
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Residues in contact with GLN 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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39A TRP* 5.3 5.5 + - - -
78A ASP* 5.7 1.7 - - - +
79A VAL* 3.0 29.7 + - + +
80A VAL* 3.2 21.0 - - + +
100A LYS* 3.1 15.8 + - - +
101A ILE* 3.1 10.3 + - - +
103A ASP* 1.3 78.0 - - + +
105A LEU* 1.3 58.6 + - - +
108A HIS* 3.4 13.4 + - - -
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Residues in contact with LEU 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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9A VAL* 4.7 4.3 - - + -
79A VAL* 3.5 43.1 - - + +
80A VAL* 3.8 11.0 - - + -
83A ALA* 3.6 20.0 - - + -
89A LEU* 5.1 0.9 - - + -
91A PHE* 4.2 20.6 - - + -
101A ILE* 3.0 35.2 + - + +
102A CYS 3.1 0.2 + - - -
104A GLN* 1.3 77.8 - - - +
106A LYS* 1.3 67.1 + - - +
107A GLY 3.1 0.5 + - - -
108A HIS* 2.9 20.2 + - + +
109A LEU* 3.9 22.1 - - + +
140A LEU* 3.9 17.3 - - + -
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Residues in contact with LYS 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 CYS 2.9 16.0 + - - +
103A ASP* 4.0 16.2 - - - +
104A GLN 3.5 1.0 - - - +
105A LEU* 1.3 74.6 - - - +
107A GLY* 1.3 59.0 - - - +
108A HIS* 3.2 18.9 + - - -
139A ARG* 3.5 29.1 + - + +
140A LEU* 3.6 9.8 - - - +
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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