Contacts of the helix formed by residues 96 - 110 (chain H) in PDB entry 1FQV
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 ASP 96 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95H VAL* 1.3 73.7 - - - +
97H GLN* 1.3 68.2 + - - +
98H GLY* 3.9 6.5 + - - +
99H THR* 2.6 40.3 + - - -
100H LEU* 3.1 10.1 + - - +
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Residues in contact with GLN 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G VAL 5.6 0.5 - - - +
109G TRP* 3.5 15.8 + - + +
95H VAL 3.8 1.0 + - - -
96H ASP* 1.3 73.6 - - - +
98H GLY* 1.3 62.9 + - - +
100H LEU* 3.3 8.2 + - - -
101H PHE* 2.8 26.6 + - - +
126H MET* 5.7 8.5 - - + -
138H THR* 2.6 49.8 + - - +
139H PHE* 3.2 24.8 - - + -
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Residues in contact with GLY 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G VAL* 5.2 16.4 - - - -
96H ASP* 3.0 9.1 + - - +
97H GLN* 1.3 79.4 - - - +
99H THR* 1.3 63.0 + - - +
101H PHE* 3.1 6.3 + - - +
102H GLU* 2.9 31.0 + - - +
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Residues in contact with THR 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H ILE* 3.9 18.9 - - + +
57H LYS* 5.0 7.9 - - + -
95H VAL* 3.6 28.6 - - + +
96H ASP* 2.6 31.1 + - - -
98H GLY* 1.3 71.2 - - - +
100H LEU* 1.3 52.7 + - - +
102H GLU* 2.9 11.8 + - - +
103H LEU* 2.7 41.8 + - + +
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TRP* 3.9 9.6 - - + -
93H LEU* 4.4 15.9 - - + +
95H VAL* 3.7 11.2 - - + +
96H ASP 3.1 9.4 + - - +
97H GLN* 3.6 9.4 - - - +
99H THR* 1.3 78.9 - - - +
101H PHE* 1.3 59.3 + - - +
103H LEU* 3.2 4.3 + - + +
104H ILE* 2.9 29.0 + - + +
119H THR* 4.2 27.1 - - + -
122H THR* 4.0 16.4 - - + -
123H VAL* 3.4 28.5 - - + -
126H MET* 3.6 31.0 - - + -
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Residues in contact with PHE 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G VAL* 5.0 15.9 - - + -
108G SER 3.5 18.6 - - - -
109G TRP* 3.5 50.2 - + + +
111G SER* 3.4 26.0 - - - -
112G LEU* 4.3 14.8 - - + +
97H GLN 2.8 18.2 + - - +
98H GLY* 3.5 5.6 - - - +
100H LEU* 1.3 75.0 - - - +
102H GLU* 1.3 74.5 + - - +
104H ILE* 3.5 3.5 + - - +
105H LEU* 3.1 60.5 + - + +
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Residues in contact with GLU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G VAL* 6.0 2.4 - - - +
54H ILE* 3.6 26.4 - - + +
98H GLY* 2.9 27.3 + - - +
99H THR* 2.9 10.5 + - - +
101H PHE* 1.3 89.2 - - - +
103H LEU* 1.3 49.1 + - - +
105H LEU* 3.2 15.4 + - - +
106H ALA* 2.7 37.0 + - - +
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Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H ILE* 3.5 28.7 - - + +
57H LYS* 4.0 25.6 - - + -
58H VAL* 4.2 10.8 - - + +
92H PHE* 4.4 10.1 - - + -
93H LEU* 3.8 29.2 - - + -
95H VAL* 4.8 2.5 - - + -
99H THR* 2.7 29.5 + - + +
100H LEU* 3.6 11.2 - - - +
102H GLU* 1.3 69.8 - - - +
104H ILE* 1.3 59.3 + - - +
105H LEU 3.0 1.8 - - - -
106H ALA* 3.7 1.7 - - - +
107H ALA* 2.7 35.0 + - - +
115H LEU* 4.1 7.5 - - + +
119H THR* 4.1 11.9 - - + -
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Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TRP* 3.7 14.6 - - + -
112G LEU* 4.5 9.0 - - + -
116G LEU* 4.3 22.4 - - + -
120G ILE* 4.6 5.8 - - + -
100H LEU* 2.9 18.2 + - + +
101H PHE* 3.9 5.6 - - - +
103H LEU* 1.3 75.0 - - - +
105H LEU* 1.3 57.3 + - - +
107H ALA* 3.7 3.3 - - - +
108H ASN* 2.9 27.5 + - - +
116H LEU* 4.5 5.5 - - + +
119H THR* 3.4 35.7 - - - +
120H CYS* 4.3 21.3 - - - +
123H VAL* 3.6 31.6 - - + -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G SER 6.0 0.2 - - - +
112G LEU* 4.1 24.0 - - + -
113G PRO* 4.7 7.9 - - + -
116G LEU* 4.6 7.9 - - + -
101H PHE* 3.1 50.3 + - + +
102H GLU* 3.3 19.5 - - - +
103H LEU 3.0 0.4 - - - -
104H ILE* 1.3 73.4 - - - +
106H ALA* 1.3 55.9 + - - +
108H ASN* 3.1 8.6 + - + +
109H TYR* 2.7 37.6 + - - +
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Residues in contact with ALA 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H ASN 5.1 2.9 - - - +
50H VAL* 4.2 19.3 - - + -
54H ILE* 3.4 26.0 - - + -
58H VAL* 4.2 11.4 - - + -
102H GLU 2.7 20.3 + - - +
103H LEU 3.7 2.2 - - - +
105H LEU* 1.3 71.2 - - - +
107H ALA* 1.3 56.8 + - - +
109H TYR* 2.9 9.0 + - - +
110H LEU* 2.7 38.7 + - - +
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Residues in contact with ALA 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H VAL* 5.2 0.8 - - - +
103H LEU 2.7 17.9 + - - +
104H ILE* 3.7 6.1 - - - +
106H ALA* 1.3 71.0 - - - +
108H ASN* 1.3 57.7 + - - +
110H LEU 3.7 0.2 - - - -
111H ASP* 2.9 21.1 + - - -
112H ILE* 2.9 25.9 + - - +
115H LEU* 3.0 37.4 - - + +
116H LEU* 4.0 20.8 - - - +
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Residues in contact with ASN 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G PRO* 5.4 4.4 - - - +
116G LEU* 3.8 34.2 - - + +
104H ILE 2.9 20.7 + - - +
105H LEU* 3.1 7.9 + - - +
107H ALA* 1.3 74.1 - - - +
109H TYR* 1.3 65.8 + - - +
111H ASP* 3.1 15.3 + - - +
116H LEU* 3.9 19.3 - - + +
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Residues in contact with TYR 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H THR* 2.6 35.1 + - + +
30H MET* 4.3 12.4 - - + +
47H LEU* 4.2 11.0 - - + +
48H PRO* 3.9 18.0 - - - +
49H ASN* 3.1 50.3 + - + +
50H VAL* 3.4 30.7 - - + -
105H LEU 2.7 20.7 + - - +
106H ALA* 3.4 3.1 - - - +
108H ASN* 1.3 75.7 - - - +
110H LEU* 1.3 63.9 + - + +
111H ASP* 3.1 1.4 + - - +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H SER* 2.5 26.5 + - - +
25H VAL 3.3 0.3 + - - -
26H THR* 3.2 16.4 + - + -
27H ILE* 3.8 20.6 - - + -
47H LEU* 3.8 22.4 - - + -
50H VAL* 4.1 13.9 - - + -
55H LEU* 5.0 7.2 - - + -
58H VAL* 3.8 35.9 - - + -
106H ALA 2.7 19.3 + - - +
109H TYR* 1.3 99.5 - - + +
111H ASP* 1.3 71.6 + - - +
112H ILE* 3.9 10.3 - - + -
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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