Contacts of the helix formed by residues 95 - 105 (chain E) in PDB entry 4QOC
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 GLU 95 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E SER* 3.3 30.7 + - - +
94E LYS* 1.3 77.4 - - + +
96E HIS* 1.3 65.2 + - - +
97E ARG 3.4 2.5 - - - -
98E LYS* 2.9 54.8 + - + +
99E ILE* 3.4 16.1 + - - +
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Residues in contact with HIS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 3.1 25.4 - - + +
93E VAL 3.1 20.1 + - - -
94E LYS* 3.2 11.4 + - - +
95E GLU* 1.3 70.7 - - - +
97E ARG* 1.3 64.4 + - - +
99E ILE* 3.2 5.3 + - + +
100E TYR* 3.0 28.2 + - - -
201E 35T 2.9 72.9 + + + -
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Residues in contact with ARG 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLN* 2.4 41.7 + - + +
19E ILE* 3.9 12.8 - - + +
95E GLU 3.4 1.2 - - - -
96E HIS* 1.3 77.7 - - - +
98E LYS* 1.3 66.7 + - + +
100E TYR* 3.3 7.2 + - + +
101E THR* 3.1 29.0 + - - +
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Residues in contact with LYS 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E GLU* 2.9 47.1 + - + +
96E HIS 3.3 0.4 - - - -
97E ARG* 1.3 75.8 - - + +
99E ILE* 1.3 60.9 + - + +
101E THR* 3.1 8.7 + - - -
102E MET* 2.9 45.7 + - + +
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Residues in contact with ILE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU* 4.6 0.4 - - + -
86E PHE* 4.8 1.7 - - + -
91E PHE* 4.1 16.6 - - + -
92E SER 3.5 23.8 - - - +
93E VAL* 4.0 10.1 - - - +
95E GLU 3.4 13.4 + - - +
96E HIS* 3.2 7.7 + - - +
98E LYS* 1.3 77.6 - - + +
100E TYR* 1.3 58.0 + - - +
102E MET* 3.4 11.3 + - + +
103E ILE* 3.0 50.5 + - + +
201E 35T 3.6 63.9 - - + -
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Residues in contact with TYR 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 3.2 40.2 - - + +
23E GLU* 3.5 38.3 - - + +
24E GLN* 3.6 15.9 + - - +
50E MET* 3.5 32.1 - - + -
54E LEU* 3.3 23.9 - - + +
96E HIS 3.0 23.5 + - - -
97E ARG* 3.6 8.3 - - + +
98E LYS 3.2 0.2 - - - -
99E ILE* 1.3 73.2 - - - +
101E THR* 1.3 66.5 + - - +
103E ILE* 4.4 3.6 - - + -
104E TYR* 3.0 34.6 + + + -
201E 35T 3.5 21.9 - + + -
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Residues in contact with THR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ARG* 3.1 17.1 + - - +
98E LYS* 3.1 12.5 + - - -
100E TYR* 1.3 79.8 - - - +
102E MET* 1.3 63.5 + - + +
103E ILE 3.3 0.2 + - - -
104E TYR* 3.4 10.9 + - - +
105E ARG* 3.1 47.7 + - - +
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Residues in contact with MET 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E LEU 4.5 1.4 - - - +
86E PHE* 3.8 53.5 - - + +
88E VAL* 3.9 22.2 - - + -
91E PHE* 4.3 23.1 - - + -
98E LYS* 2.9 40.3 + - + +
99E ILE* 3.7 14.4 - - + +
101E THR* 1.3 77.8 - - - +
103E ILE* 1.3 59.2 + - - +
105E ARG* 3.5 23.4 + - - +
106E ASN* 3.0 21.1 - - - +
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Residues in contact with ILE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.7 5.6 - - + -
50E MET* 4.0 17.9 - - + -
53E VAL* 4.3 11.7 - - + -
54E LEU* 3.7 27.8 - - + -
57E LEU* 3.7 21.8 - - + -
86E PHE* 3.8 21.5 - - + -
99E ILE* 3.0 34.9 + - + +
100E TYR* 3.8 6.1 - - - +
101E THR 3.3 0.2 - - - -
102E MET* 1.3 76.5 - - - +
104E TYR* 1.3 61.7 + - + +
106E ASN* 2.8 27.1 + - - +
107E LEU* 3.5 25.0 - - + +
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Residues in contact with TYR 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLU* 3.5 29.4 + - - -
26E THR* 3.4 27.0 - - - +
28E VAL* 4.7 0.4 - - + -
31E LYS* 5.2 0.2 + - - -
50E MET* 3.8 26.6 - - + +
100E TYR* 3.0 29.5 + + - +
101E THR* 3.4 6.0 + - - +
103E ILE* 1.3 79.1 - - + +
105E ARG* 1.3 57.2 + - - +
106E ASN 3.0 0.7 - - - -
107E LEU* 3.0 43.3 - - + +
109E VAL* 3.5 27.4 - - + -
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Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LYS* 3.1 23.3 + - - +
85E LEU 5.4 2.5 - - - +
86E PHE 5.1 5.7 + - - -
101E THR* 3.1 45.8 + - - +
102E MET* 3.8 22.0 - - - +
103E ILE 3.1 1.0 - - - -
104E TYR* 1.3 77.0 - - - +
106E ASN* 1.3 62.8 + - - +
107E LEU 3.5 0.4 - - - -
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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