Contacts of the helix formed by residues 99 - 112 (chain B) in PDB entry 4CEV
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 HIS 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A ORN 4.8 0.2 - - - +
98B ASP* 1.3 67.6 - - - +
100B SER* 1.3 60.8 + - - +
101B ILE 3.0 7.8 + - - -
102B ALA* 3.0 21.2 + - + +
120B TRP* 3.2 26.2 - + - -
122B ASP* 3.0 17.3 - - - -
126B ASP* 3.0 2.9 + - - -
139B HIS* 3.8 14.1 - - - +
142B PRO* 3.4 7.0 - - + +
224B SER* 2.8 29.8 + - - -
226B ASP* 3.4 20.2 + - + +
270B VAL* 3.5 22.8 - - + +
271B GLU* 2.9 15.8 + - + +
300B MN 2.1 32.1 + - - +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 3.8 9.9 - - - +
14B GLY* 3.8 5.4 - - - -
71B VAL* 3.8 15.4 - - - +
75B ASN* 3.2 16.0 + - - +
98B ASP* 2.7 24.1 + - - -
99B HIS* 1.3 77.5 - - - +
101B ILE* 1.3 60.4 + - - +
102B ALA 3.1 2.2 + - - -
103B ILE* 3.3 14.5 + - - +
138B ILE* 3.9 23.3 - - - -
139B HIS* 3.7 18.6 - - - +
142B PRO* 4.2 6.5 - - - -
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Residues in contact with ILE 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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9B VAL* 3.5 27.1 - - + +
11B MET* 3.6 25.6 - - + -
75B ASN* 3.3 8.3 - - - +
78B LEU* 3.2 14.2 - - + +
94B VAL* 3.6 25.6 - - + -
96B GLY* 3.6 30.3 - - - +
98B ASP 3.4 16.6 - - - +
99B HIS 3.0 1.0 - - - -
100B SER* 1.3 75.4 - - - +
102B ALA* 1.3 66.9 + - - +
103B ILE 3.0 2.5 - - - -
104B GLY 3.1 10.2 + - - -
105B THR* 3.2 10.9 + - - -
268B GLU* 3.9 3.4 - - - +
270B VAL* 3.8 19.1 - - + -
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Residues in contact with ALA 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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99B HIS* 3.0 19.4 + - + +
101B ILE* 1.3 80.2 - - - +
103B ILE* 1.3 62.1 + - - +
106B LEU* 2.9 32.0 + - + +
120B TRP* 3.5 30.5 - - + -
142B PRO* 3.9 3.1 - - + -
146B SER* 4.7 1.8 - - - -
268B GLU* 3.2 28.5 - - - +
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Residues in contact with ILE 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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75B ASN* 3.9 7.9 - - + +
100B SER 3.4 17.0 - - - +
101B ILE 3.0 0.2 - - - -
102B ALA* 1.3 76.9 - - - +
104B GLY* 1.3 57.3 + - - +
106B LEU* 4.2 1.4 - - - +
107B ALA* 3.1 25.6 + - - +
138B ILE* 4.3 14.6 - - + -
142B PRO* 3.6 33.0 - - + +
145B ALA* 4.1 14.1 - - + -
146B SER* 4.2 11.2 + - - +
154B LEU* 3.5 46.9 - - + +
157B ILE* 3.7 17.0 - - + -
163B LYS* 5.1 3.3 - - - +
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 2.8 43.8 + - - -
78B LEU* 3.9 11.2 - - - -
79B ALA* 3.2 12.4 - - - -
101B ILE 3.1 0.6 + - - -
103B ILE* 1.3 75.5 - - - +
105B THR* 1.3 63.0 + - - +
107B ALA* 3.2 4.5 + - - +
108B GLY* 3.1 17.5 + - - -
157B ILE* 4.6 0.4 - - - -
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Residues in contact with THR 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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78B LEU* 3.6 10.4 - - - +
82B VAL* 3.7 14.2 - - + +
92B PRO* 5.7 1.3 - - + -
94B VAL* 3.6 26.7 - - + +
101B ILE 3.2 8.7 + - - -
102B ALA 3.8 3.8 - - - -
104B GLY* 1.3 74.7 - - - +
106B LEU* 1.3 62.2 + - - +
108B GLY 3.1 3.1 + - - -
109B VAL* 3.1 30.0 + - + +
222B HIS* 3.5 29.6 - - + +
266B SER* 5.4 1.6 - - - +
267B ALA 5.0 1.1 - - - +
268B GLU* 2.7 25.7 + - - +
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Residues in contact with LEU 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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102B ALA* 2.9 17.5 + - + +
103B ILE 4.5 0.7 - - - +
105B THR* 1.3 77.3 - - - +
107B ALA* 1.3 57.9 + - - +
109B VAL* 4.5 3.6 - - + +
110B ALA* 3.0 35.9 + - - +
116B LEU* 3.8 26.9 - - + -
118B VAL* 4.0 10.8 - - + -
120B TRP* 4.3 22.0 - - + -
146B SER* 3.4 32.5 - - - +
163B LYS* 3.9 10.3 - - + -
164B ILE* 4.3 14.1 - - + -
222B HIS* 3.6 31.2 - - + +
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Residues in contact with ALA 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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79B ALA* 3.8 16.7 - - + +
103B ILE 3.1 21.6 + - - +
104B GLY 3.2 7.1 + - - +
105B THR 3.1 0.4 - - - -
106B LEU* 1.3 74.0 - - - +
108B GLY* 1.3 56.3 + - - +
111B LYS* 3.6 6.9 + - - -
157B ILE* 3.8 26.7 - - + +
158B GLY* 4.7 0.9 - - - +
160B TYR* 2.4 36.1 + - - -
163B LYS* 3.9 10.5 - - - +
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Residues in contact with GLY 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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79B ALA* 3.4 23.8 - - - +
82B VAL* 3.9 5.4 - - - -
83B ASP* 3.4 16.9 - - - +
86B VAL* 4.2 1.2 - - - +
104B GLY 3.1 9.7 + - - -
105B THR 3.1 4.4 + - - -
107B ALA* 1.3 76.5 - - - +
109B VAL* 1.3 62.0 + - - +
111B LYS* 3.9 3.2 - - - +
112B HIS* 3.0 25.6 + - - -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 3.4 19.1 - - + -
86B VAL* 4.2 5.8 - - + -
92B PRO* 4.0 18.2 - - + -
105B THR* 3.1 21.6 + - + +
106B LEU* 4.3 4.9 - - + +
108B GLY* 1.3 78.3 - - - +
110B ALA* 1.3 67.3 + - - +
111B LYS 3.3 1.8 - - - -
112B HIS* 3.0 18.4 + - - +
113B TYR* 3.2 30.0 - - + +
116B LEU* 4.0 15.7 - - + -
222B HIS* 5.2 0.4 - - + +
266B SER* 3.8 24.2 - - - +
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Residues in contact with ALA 110 (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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106B LEU 3.0 19.0 + - - +
109B VAL* 1.3 73.6 - - - +
111B LYS* 1.3 63.0 + - - +
112B HIS 2.9 7.3 + - - -
113B TYR* 2.9 23.8 + - - +
116B LEU* 3.8 23.0 - - + +
160B TYR* 3.6 7.2 - - + +
163B LYS* 3.2 36.5 - - + +
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Residues in contact with LYS 111 (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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79B ALA* 5.4 0.8 + - - +
83B ASP* 3.4 30.2 + - - +
87B GLN* 5.5 1.1 - - - +
107B ALA 3.6 15.8 + - - -
108B GLY* 3.9 5.1 - - - +
110B ALA* 1.3 73.9 - - - +
112B HIS* 1.3 92.2 + - + +
113B TYR 3.3 2.6 + - - +
158B GLY* 4.6 9.5 + - - -
160B TYR* 3.1 37.3 + - + +
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Residues in contact with HIS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP* 2.6 34.5 + - - -
86B VAL* 3.5 27.3 - - + +
87B GLN* 3.8 23.3 - - + -
108B GLY 3.0 24.2 + - - -
109B VAL 3.3 10.5 - - - +
110B ALA 2.9 1.8 + - - -
111B LYS* 1.3 90.2 - - + +
113B TYR* 1.3 72.4 + - + +
114B GLU* 6.0 1.1 - - - -
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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