Contacts of the helix formed by residues 99 - 107 (chain A) in PDB entry 4FZY
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 THR 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A VAL* 3.9 22.0 - - + -
79A ALA 3.4 3.6 + - - -
80A HIS* 3.0 41.3 + - - +
97A ILE 4.0 1.2 + - - -
98A CYS* 1.3 68.8 - - - +
100A MET* 1.3 58.9 + - - +
102A LEU* 3.7 8.8 - - + +
103A ALA* 2.9 30.7 + - - +
143A THR* 3.8 7.7 - - + +
146A LEU* 3.8 16.3 - - + +
147A LEU* 4.2 25.4 - - + -
150A ILE* 3.8 9.5 - - + +
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Residues in contact with MET 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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80A HIS* 3.5 15.6 + - + -
81A ASN* 3.5 40.1 - - - +
98A CYS* 3.2 14.0 - - - -
99A THR* 1.3 83.0 + - - +
101A LYS* 1.3 70.6 + - + +
103A ALA* 3.6 3.2 - - - +
104A ARG* 2.9 42.9 + - + +
112A TYR* 3.9 20.7 - - + +
10C G 3.7 35.0 - - - +
6D A 6.4 3.1 - - - -
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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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98A CYS* 3.3 25.5 + - + +
100A MET* 1.3 87.3 - - + +
102A LEU* 1.3 61.9 + - - +
104A ARG* 3.3 13.7 + - - +
105A ARG* 3.1 24.3 + - - +
164A ILE* 3.0 28.6 + - + +
165A THR* 3.3 29.8 - - + +
166A GLY* 5.8 0.2 - - - -
6D A 3.2 45.2 + - - -
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Residues in contact with LEU 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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97A ILE* 3.6 26.7 - - + -
98A CYS 3.1 14.6 + - - +
99A THR* 3.8 15.3 - - + +
101A LYS* 1.3 75.5 - - - +
103A ALA* 1.3 57.9 + - - +
105A ARG* 3.4 4.1 + - - +
106A LEU* 2.9 31.5 + - - +
147A LEU* 4.7 1.1 - - + -
150A ILE* 3.9 22.4 - - + -
156A TRP* 4.0 7.7 - - + -
161A MET* 3.6 46.7 - - + +
164A ILE* 3.8 28.9 - - + -
165A THR* 4.6 1.6 - - - +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A THR 2.9 19.2 + - - +
100A MET 3.6 3.4 - - - +
102A LEU* 1.3 72.5 - - - +
104A ARG* 1.3 60.2 + - - +
107A TRP* 2.8 53.0 + - + +
112A TYR* 3.7 16.7 - - + -
117A LEU* 4.1 22.0 - - + -
146A LEU* 5.0 0.7 - - + -
150A ILE* 4.0 9.8 - - + +
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Residues in contact with ARG 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 MET* 2.9 35.9 + - - +
101A LYS* 3.4 17.3 - - - +
103A ALA* 1.3 79.7 - - - +
105A ARG* 1.3 59.4 + - - +
108A PRO* 3.6 23.0 - - - +
112A TYR* 3.5 48.7 + - + +
9C C 4.4 27.3 + - - -
10C G 4.4 6.1 + - - -
6D A 4.1 23.7 + - - -
7D T 4.0 35.4 + - - +
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Residues in contact with ARG 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* 3.1 15.5 + - - +
102A LEU 3.9 3.4 - - - +
104A ARG* 1.3 78.0 - - - +
106A LEU* 1.3 66.3 + - - +
108A PRO* 4.3 6.2 - - - +
156A TRP* 3.8 22.5 - - + -
164A ILE* 4.0 43.5 + - + +
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Residues in contact with LEU 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 LEU 2.9 16.9 + - - +
103A ALA 4.0 1.6 - - - +
105A ARG* 1.3 79.6 - - - +
107A TRP* 1.3 108.4 + - + +
108A PRO* 3.7 5.6 - - - +
150A ILE* 3.8 30.7 - - + +
153A THR* 4.2 11.7 - - + +
154A SER* 3.9 24.5 - - - -
156A TRP* 4.2 12.3 - - + -
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Residues in contact with TRP 107 (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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103A ALA* 2.8 30.7 + - + +
104A ARG 3.8 0.4 - - - -
106A LEU* 1.3 115.1 - - + +
108A PRO* 1.3 61.2 - - - +
110A ILE* 3.5 23.7 - - + +
112A TYR* 2.6 30.9 + - - -
117A LEU* 5.1 1.6 - - + -
121A ARG* 3.2 64.1 - - + +
146A LEU* 4.3 7.9 - - + -
149A ASP* 3.4 10.5 - - - -
150A ILE* 3.9 25.1 - - + -
153A THR* 4.1 14.4 - - + +
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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