Contacts of the helix formed by residues 96 - 108 (chain B) in PDB entry 4CQM
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 LYS 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ARG 3.8 3.2 + - - -
95B THR* 1.3 78.7 - - - +
97B THR* 1.3 66.1 + - - +
98B GLU* 3.2 26.8 + - + +
99B ASP* 3.3 20.7 + - - +
100B MET* 3.4 11.8 + - - +
116C LYS* 4.1 4.5 - - - +
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR 3.8 1.2 + - - -
96B LYS* 1.3 73.8 - - - +
98B GLU* 1.3 63.6 + - - +
100B MET* 3.1 10.3 + - - +
101B VAL* 3.0 35.5 + - + +
60C GLU* 3.3 51.6 + - + +
109C LEU* 4.7 5.2 - - + -
113C LEU* 3.6 26.2 - - + +
116C LYS* 4.2 7.4 + - - +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 4.0 18.6 - - + +
97B THR* 1.3 80.5 - - - +
99B ASP* 1.3 65.7 + - - +
101B VAL* 3.4 7.1 + - - +
102B SER* 3.0 25.9 + - - -
60C GLU* 5.0 3.5 + - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ARG* 5.6 12.8 - - + +
95B THR* 4.4 10.9 - - + +
96B LYS* 3.3 18.9 + - - +
97B THR 3.3 0.4 - - - -
98B GLU* 1.3 82.7 - - - +
100B MET* 1.3 64.8 + - - +
102B SER* 3.4 10.5 - - - -
103B GLN* 3.1 31.5 + - + +
147B VAL* 4.2 1.5 - - - +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.6 7.9 - - + -
95B THR* 3.7 26.2 - - + +
96B LYS 3.4 16.4 - - - +
97B THR* 3.1 16.8 + - - +
99B ASP* 1.3 79.0 - - - +
101B VAL* 1.3 60.3 + - - +
104B LEU* 3.3 31.9 + - - +
147B VAL* 4.0 13.3 - - + +
109C LEU* 3.7 13.5 - - + -
112C MET* 3.6 49.4 - - + +
113C LEU* 3.7 25.1 - - + -
116C LYS* 4.5 7.6 - - - -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR* 3.0 22.8 + - + +
98B GLU* 3.7 8.1 - - - +
100B MET* 1.3 75.4 - - - +
102B SER* 1.3 65.0 + - - +
104B LEU* 3.3 6.2 + - - -
105B HIS* 3.0 58.3 + - + +
105C HIS* 4.0 10.8 - - + +
109C LEU* 3.9 26.2 - - + -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.5 17.0 - - - +
98B GLU 3.0 15.7 + - - -
99B ASP* 3.2 18.1 + - - -
101B VAL* 1.3 77.8 - - - +
103B GLN* 1.3 58.4 + - - +
105B HIS* 3.5 3.4 + - - +
106B THR* 2.8 34.4 + - - -
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.5 29.5 - - + +
87B ASN* 4.5 0.4 + - - -
88B ARG* 3.0 46.5 + - + +
99B ASP* 3.1 16.8 + - + +
102B SER* 1.3 75.2 - - - +
104B LEU* 1.3 59.5 + - - +
107B ASN* 2.9 40.3 + - - +
147B VAL* 3.6 29.6 - - + +
148B TYR* 3.4 37.2 - - - -
151B SER* 3.5 4.7 - - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET 3.3 24.7 + - - +
101B VAL* 3.3 7.4 + - - +
102B SER 3.3 0.4 - - - -
103B GLN* 1.3 80.0 - - - +
105B HIS* 1.3 62.2 + - + +
108B LEU* 3.2 11.6 + - + +
109B LEU* 3.0 23.7 + - - +
147B VAL* 4.6 4.5 - - + +
151B SER* 4.1 24.9 - - - +
104C LEU* 4.0 23.8 - - + +
105C HIS* 4.8 6.5 - - + -
108C LEU* 4.4 12.6 - - + -
109C LEU* 3.8 37.9 - - + +
112C MET* 4.1 21.5 - - + -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ALA* 4.0 27.1 + - + +
101B VAL* 3.0 42.4 + - + +
102B SER* 4.0 4.0 - - - +
104B LEU* 1.3 80.8 - - + +
106B THR* 1.3 57.9 + - - +
109B LEU* 3.4 19.0 - - + +
110B GLY* 2.6 33.1 + - - -
101C VAL* 4.2 22.9 - - + +
104C LEU* 5.6 1.1 - - + -
105C HIS* 2.9 31.8 + + - -
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 6.4 1.1 - - - +
56B ASP* 5.5 1.6 + - - +
57B VAL* 3.7 29.8 - - + +
58B ALA* 4.5 9.9 - - - +
84B ALA* 3.9 6.7 - - + +
85B GLY* 4.1 13.0 - - - +
86B ILE* 3.4 32.6 - - + +
102B SER* 2.8 22.4 + - - -
103B GLN 4.2 0.2 - - - -
105B HIS* 1.3 79.9 - - - +
107B ASN* 1.3 71.4 + - - +
110B GLY* 3.8 5.4 - - - -
111B SER* 4.3 1.9 + - - -
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA 4.6 2.2 - - - +
85B GLY* 3.2 7.4 - - - -
86B ILE 3.0 43.4 + - - -
103B GLN* 2.9 26.6 + - - +
106B THR* 1.3 79.1 - - - +
108B LEU* 1.3 57.9 + - - +
111B SER* 3.2 18.4 + - - -
148B TYR* 3.7 9.5 - - - -
151B SER* 3.1 28.2 + - - +
152B LYS* 3.4 24.2 + - + +
155B LEU* 3.5 15.4 - - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.2 14.3 + - + +
107B ASN* 1.3 79.8 - - - +
109B LEU* 1.3 68.1 + - - +
110B GLY 3.2 0.7 - - - -
111B SER* 3.2 4.2 + - - -
112B MET* 3.1 32.7 + - + +
151B SER* 3.6 20.4 - - - +
154B GLY* 3.7 29.6 - - - +
155B LEU* 4.0 10.8 - - + +
158B PHE* 4.9 1.3 - - + -
104C LEU* 3.6 34.3 - - + -
108C LEU* 4.0 13.0 - - + -
150C ALA* 3.8 24.5 - - + +
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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