Contacts of the helix formed by residues 112 - 128 (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 ILE 112 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H GLN* 4.2 14.1 - - + +
24H SER* 3.8 17.7 - - - -
58H VAL* 3.3 34.3 - - + -
61H TRP* 4.4 9.0 - - + -
62H CYS* 4.1 13.0 - - - -
107H ALA* 2.9 16.4 + - - +
110H LEU* 3.8 26.2 - - + +
111H ASP* 1.3 73.9 - - - +
113H LYS* 1.3 64.2 + - - +
114H GLY* 3.0 3.5 + - - +
115H LEU* 3.8 24.7 - - + +
116H LEU* 2.8 24.3 + - - +
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Residues in contact with LYS 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H ASP* 3.7 10.2 + - - +
112H ILE* 1.3 71.7 - - - +
114H GLY* 1.3 67.4 + - - +
116H LEU* 4.1 14.4 - - + -
117H ASP* 3.0 46.2 + - - +
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Residues in contact with GLY 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H TRP* 3.4 18.7 - - - -
112H ILE* 3.0 4.1 + - - +
113H LYS* 1.3 84.7 - - - +
115H LEU* 1.3 61.5 + - - +
117H ASP* 3.0 18.1 + - - +
118H VAL* 3.4 7.6 + - - +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H VAL* 5.4 9.4 - - + -
61H TRP* 3.3 59.6 - - + +
92H PHE* 4.0 11.2 - - + -
93H LEU* 5.0 0.2 - - + -
103H LEU* 4.1 16.2 - - + +
107H ALA* 3.0 33.9 - - + -
112H ILE* 3.2 17.7 + - + +
114H GLY* 1.3 71.3 - - - +
116H LEU* 1.3 61.8 + - - +
118H VAL* 3.4 10.0 - - + +
119H THR* 2.9 43.5 + - + +
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.5 14.4 - - + -
104H ILE* 4.5 7.4 - - + +
107H ALA* 4.0 15.9 - - + +
108H ASN* 3.9 31.0 - - - +
111H ASP* 5.4 6.3 - - - +
112H ILE 2.8 18.3 + - - +
113H LYS* 3.7 16.2 - - + +
115H LEU* 1.3 76.7 - - - +
117H ASP* 1.3 63.4 + - - +
119H THR* 2.8 19.5 + - - +
120H CYS* 3.0 42.1 + - - -
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Residues in contact with ASP 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G CYS* 5.4 1.2 - - - -
113H LYS* 3.0 33.4 + - - +
114H GLY* 3.0 12.5 + - - +
116H LEU* 1.3 77.7 - - - +
118H VAL* 1.3 68.8 + - - +
120H CYS* 3.3 4.8 + - - +
121H LYS* 2.9 67.0 + - - +
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Residues in contact with VAL 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H TRP* 3.8 21.3 - - + +
85H ILE* 4.1 22.1 - - + +
86H PRO* 4.9 3.4 - - + -
89H ASP* 3.5 21.1 - - - +
93H LEU* 4.2 11.4 - - + -
114H GLY 3.7 9.6 - - - +
115H LEU* 3.4 23.6 - - + +
117H ASP* 1.3 82.8 - - - +
119H THR* 1.3 52.4 + - - +
121H LYS* 3.0 6.7 + - + +
122H THR* 2.5 43.5 + - - +
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU* 4.0 15.7 - - + -
100H LEU* 4.2 4.8 - - + +
103H LEU* 4.1 18.4 - - + -
104H ILE* 3.4 28.0 - - + +
115H LEU* 2.9 38.6 + - + +
116H LEU* 2.8 24.4 + - - -
118H VAL* 1.3 75.3 - - - +
120H CYS* 1.3 60.7 + - - +
122H THR* 3.2 10.2 + - - -
123H VAL* 3.1 27.0 + - - +
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Residues in contact with CYS 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.8 7.2 - - - -
119G GLY* 4.7 4.7 - - - -
120G ILE* 3.9 36.6 - - + +
123G CYS* 4.2 9.1 - - - -
104H ILE* 4.3 17.7 - - - -
116H LEU* 3.0 43.3 + - - +
117H ASP* 3.8 4.3 - - - +
118H VAL 3.2 0.2 - - - -
119H THR* 1.3 81.3 + - - +
121H LYS* 1.3 58.2 + - - +
123H VAL* 3.4 3.1 + - - +
124H ALA* 3.0 25.1 + - - +
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Residues in contact with LYS 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G CYS* 3.4 26.2 - - + -
85H ILE* 4.0 18.2 - - + -
117H ASP* 2.9 53.7 + - - +
118H VAL* 3.6 5.6 - - + +
120H CYS* 1.3 75.2 - - - +
122H THR* 1.3 60.2 + - - +
124H ALA* 3.4 4.4 - - - +
125H ASN* 2.8 34.2 + - - +
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Residues in contact with THR 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H ILE* 3.6 14.6 - - - +
93H LEU* 3.0 36.1 - - + +
100H LEU* 4.0 19.1 - - + -
118H VAL 2.5 22.7 + - - -
119H THR 3.2 7.6 - - - -
120H CYS 3.2 0.2 - - - -
121H LYS* 1.3 79.9 - - - +
123H VAL* 1.3 57.7 + - - +
125H ASN* 3.4 7.1 + - - +
126H MET* 3.1 37.7 + - + +
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Residues in contact with VAL 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G TRP* 3.6 13.2 - - + -
120G ILE* 3.6 29.6 - - + -
139G TRP* 6.2 0.7 - - + -
100H LEU* 3.4 27.4 - - + -
104H ILE* 3.6 18.2 - - + -
119H THR 3.1 15.0 + - - +
120H CYS 3.8 7.0 - - - +
122H THR* 1.3 72.9 - - - +
124H ALA* 1.3 66.4 + - - +
126H MET* 3.2 9.8 + - - +
127H ILE* 3.1 24.8 + - + +
139H PHE* 3.8 21.1 - - + -
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Residues in contact with ALA 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ILE* 3.9 8.5 - - - +
123G CYS* 3.4 36.8 - - + +
124G LEU* 3.6 18.7 - - + +
120H CYS 3.0 10.5 + - - +
121H LYS* 3.2 8.3 + - - +
123H VAL* 1.3 79.1 - - - +
125H ASN* 1.3 57.6 + - - +
127H ILE* 3.2 5.4 + - - +
128H LYS* 3.0 34.9 + - - +
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Residues in contact with ASN 125 (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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85H ILE* 3.9 18.4 - - - +
121H LYS* 2.8 20.8 + - - +
122H THR* 3.6 7.6 - - - +
123H VAL 3.2 0.2 - - - -
124H ALA* 1.3 78.6 - - - +
126H MET* 1.3 60.7 + - + +
128H LYS* 3.4 44.1 + - - +
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Residues in contact with MET 126 (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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93H LEU 5.3 4.0 - - - +
95H VAL 5.2 9.0 - - - +
97H GLN* 5.7 9.2 - - + -
100H LEU* 3.6 28.3 - - + -
122H THR* 3.1 23.9 + - + +
123H VAL* 3.5 7.6 - - - +
124H ALA 3.2 0.4 - - - -
125H ASN* 1.3 77.9 - - - +
127H ILE* 1.3 61.3 + - - +
128H LYS 3.4 6.1 - - - +
130H LYS* 3.3 32.8 - - - +
139H PHE* 3.8 32.1 - - + -
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Residues in contact with ILE 127 (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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120G ILE* 4.1 21.1 - - + -
121G PHE* 4.7 2.0 - - + -
124G LEU* 4.2 13.2 - - + -
128G GLU* 5.1 0.9 - - + +
131G LYS* 2.6 27.7 + - - +
132G VAL* 3.1 32.3 - - + -
139G TRP* 3.8 28.7 - - + -
123H VAL* 3.1 16.0 + - + +
124H ALA* 3.2 8.7 + - - +
126H MET* 1.3 73.6 - - - +
128H LYS* 1.3 58.0 + - - +
130H LYS* 3.3 11.3 + - - +
135H ILE* 3.4 17.9 - - + +
139H PHE* 3.7 19.3 - - + -
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Residues in contact with LYS 128 (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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123G CYS 3.5 23.3 + - - -
124G LEU* 3.8 4.6 - - + +
125G CYS* 3.6 26.5 - - - +
128G GLU* 3.5 22.8 - - + +
131G LYS* 3.4 5.6 - - - +
124H ALA* 3.0 21.0 + - - +
125H ASN* 3.5 39.6 - - - +
126H MET 3.2 7.8 - - - +
127H ILE* 1.3 79.2 - - - +
129H GLY* 1.3 59.2 + - - +
130H LYS* 3.2 4.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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