Contacts of the helix formed by residues 99 - 112 (chain F) in PDB entry 1CEV
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F GLY 3.5 0.2 + - - -
98F ASP* 1.3 70.6 - - - +
100F SER* 1.3 62.3 + - - +
101F ILE* 3.0 2.2 - - - -
102F ALA* 3.0 22.1 + - + +
120F TRP* 3.3 24.0 - + - -
122F ASP* 2.8 14.5 + - - -
126F ASP* 3.6 4.0 - - - +
139F HIS* 4.1 5.7 - - - +
142F PRO* 3.3 7.3 - - - +
224F SER* 2.7 38.0 + - - -
226F ASP* 3.3 18.9 + - + +
268F GLU* 4.7 1.1 - - - -
270F VAL* 3.6 23.1 - - + +
271F GLU* 2.8 15.7 + - + +
300F MN 2.5 35.4 + - - +
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Residues in contact with SER 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET* 4.1 13.2 - - - -
71F VAL* 4.4 7.1 - - - +
75F ASN* 3.3 7.9 + - - +
98F ASP* 3.5 14.1 + - - +
99F HIS* 1.3 78.2 - - - +
101F ILE* 1.3 60.7 + - - +
102F ALA 3.0 0.9 - - - -
103F ILE* 3.1 24.9 + - - +
138F ILE* 3.4 17.6 - - - +
139F HIS* 3.0 34.7 + - - +
142F PRO* 4.0 10.1 - - - -
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Residues in contact with ILE 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.6 28.9 - - + +
11F MET* 4.0 24.2 - - + -
75F ASN* 3.2 9.0 - - - +
78F LEU* 3.3 10.9 - - + +
94F VAL* 3.9 22.7 - - + -
96F GLY* 3.6 31.0 - - - -
98F ASP 3.2 16.4 - - - +
99F HIS 3.0 1.5 - - - -
100F SER* 1.3 72.6 - - - +
102F ALA* 1.3 60.6 + - - +
103F ILE 3.0 2.9 - - - -
104F GLY 3.0 2.9 + - - -
105F THR* 2.9 27.8 + - - -
268F GLU* 4.0 3.8 - - - +
270F VAL* 3.6 19.3 - - + -
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F HIS* 3.0 20.5 + - + +
101F ILE* 1.3 80.2 - - - +
103F ILE* 1.3 57.1 + - - +
105F THR* 4.3 0.2 - - - -
106F LEU* 2.9 39.5 + - + +
120F TRP* 3.5 31.2 - - + -
142F PRO* 4.1 2.9 - - + +
146F SER* 4.5 0.4 - - - -
268F GLU* 3.2 28.3 - - - +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ASN* 3.9 9.9 - - + +
100F SER 3.3 15.3 - - - +
102F ALA* 1.3 79.3 - - - +
104F GLY* 1.3 57.1 + - - +
106F LEU* 4.0 1.2 - - - +
107F ALA* 3.0 30.5 + - - +
138F ILE* 4.0 25.6 - - + -
142F PRO* 3.8 29.2 - - + +
145F ALA* 4.2 16.4 - - + -
146F SER* 3.9 10.3 + - - +
154F LEU* 3.6 34.5 - - + +
157F ILE* 3.7 19.1 - - + -
163F LYS* 5.1 3.5 - - - +
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Residues in contact with GLY 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ASN* 2.8 45.5 + - - -
78F LEU* 4.0 10.5 - - - -
79F ALA* 3.3 10.3 - - - -
82F VAL* 4.8 0.2 - - - +
101F ILE 3.0 1.3 + - - -
103F ILE* 1.3 72.8 - - - +
105F THR* 1.3 64.6 + - - +
107F ALA* 3.2 5.1 + - - +
108F GLY* 3.1 18.4 + - - -
157F ILE* 4.8 0.4 - - - -
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Residues in contact with THR 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F LEU* 3.6 10.3 - - - +
82F VAL* 3.7 13.7 - - + +
92F PRO* 5.7 1.6 - - + -
94F VAL* 3.7 26.2 - - + +
101F ILE 2.9 10.2 + - - -
102F ALA 4.0 1.3 - - - -
104F GLY* 1.3 75.7 - - - +
106F LEU* 1.3 62.1 + - - +
108F GLY 3.3 1.4 + - - -
109F VAL* 3.1 36.4 + - + +
222F HIS* 3.5 28.5 - - + +
266F SER* 5.3 1.6 - - - +
267F ALA 4.9 1.1 - - - +
268F GLU* 2.7 27.2 + - + +
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ALA* 2.9 20.0 + - + +
103F ILE 4.2 2.0 - - - +
105F THR* 1.3 74.0 - - - +
107F ALA* 1.3 61.1 + - - +
109F VAL* 4.5 2.9 - - + +
110F ALA* 2.9 35.7 + - + +
116F LEU* 3.7 27.8 - - + -
118F VAL* 3.9 12.8 - - + -
120F TRP* 4.5 19.1 - - + -
146F SER* 3.5 30.1 - - - +
163F LYS* 3.9 11.4 - - + -
164F ILE* 4.5 13.0 - - + -
222F HIS* 3.7 30.3 - - + +
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Residues in contact with ALA 107 (chain F).
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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79F ALA* 3.6 16.8 - - + -
103F ILE 3.0 19.1 + - - +
104F GLY 3.2 5.6 + - - +
106F LEU* 1.3 76.4 - - - +
108F GLY* 1.3 60.3 + - - +
111F LYS* 4.0 5.9 - - - -
157F ILE* 3.7 29.2 - - + +
158F GLY* 4.3 1.9 - - - -
160F TYR* 2.6 31.2 + - - -
163F LYS* 3.8 11.8 - - - +
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Residues in contact with GLY 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F ALA* 3.3 25.5 - - - +
82F VAL* 3.8 12.6 - - - -
83F ASP* 3.5 9.6 - - - -
86F VAL* 4.4 0.7 - - - +
104F GLY 3.1 10.7 + - - -
105F THR 3.3 2.4 + - - -
106F LEU 3.2 0.2 - - - -
107F ALA* 1.3 79.3 - - - +
109F VAL* 1.3 56.1 + - - +
111F LYS* 3.8 3.3 - - - +
112F HIS* 3.1 28.1 + - - -
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Residues in contact with VAL 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F VAL* 3.4 18.2 - - + -
86F VAL* 4.4 6.1 - - + -
92F PRO* 4.1 6.3 - - + -
105F THR* 3.1 22.7 + - + +
106F LEU* 4.2 4.5 - - + +
108F GLY* 1.3 74.4 - - - +
110F ALA* 1.3 68.3 + - - +
111F LYS 3.3 2.0 - - - -
112F HIS* 2.8 26.5 + - - +
113F TYR* 3.5 23.5 - - + -
116F LEU* 4.0 14.6 - - + -
222F HIS* 5.1 0.2 - - - +
266F SER* 3.7 35.9 - - - +
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Residues in contact with ALA 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU 2.9 21.2 + - - +
109F VAL* 1.3 73.0 - - - +
111F LYS* 1.3 52.8 + - - +
112F HIS 2.8 0.3 + - - -
113F TYR* 2.7 38.4 + - - +
116F LEU* 3.7 22.4 - - + +
160F TYR* 3.4 8.1 - - + +
163F LYS* 3.3 37.0 - - + +
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Residues in contact with LYS 111 (chain F).
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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83F ASP* 3.1 24.4 + - - +
107F ALA 4.0 6.3 - - - -
108F GLY* 3.8 5.8 - - - +
110F ALA* 1.3 71.8 - - - +
112F HIS* 1.3 86.4 + - + +
113F TYR 3.3 4.0 + - - +
158F GLY* 4.3 10.4 + - - -
160F TYR* 2.8 45.7 + - + +
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Residues in contact with HIS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ASP* 2.7 40.7 + - - -
86F VAL* 3.5 29.4 - - + +
87F GLN* 4.0 17.1 + - - +
108F GLY 3.1 23.7 + - - -
109F VAL 2.8 10.6 + - - +
110F ALA 2.8 0.4 + - - -
111F LYS* 1.3 88.9 - - + +
113F TYR* 1.3 74.1 - - + +
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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