Contacts of the helix formed by residues 103 - 118 (chain B) in PDB entry 1F1H
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B PHE* 6.0 0.9 - - - +
22B THR 4.7 2.9 + - - +
57B TRP* 4.4 4.0 - - - -
89B CYS 5.6 0.3 - - - +
90B ASP* 3.7 5.0 - - - -
91B ILE* 2.8 42.6 + - + +
100B TYR* 3.1 28.3 + - + +
101B ASP 3.4 0.4 - - - -
102B ARG* 1.3 74.1 - - - +
104B PRO* 1.3 72.9 - - - +
105B ARG* 2.9 16.6 + - - +
106B SER* 2.9 24.4 + - - +
107B ILE* 3.0 24.2 + - - +
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Residues in contact with PRO 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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22B THR* 3.6 16.2 - - + +
23B ASP 3.5 24.7 - - - +
24B THR* 4.1 4.5 - - - -
57B TRP* 3.9 5.6 - - + -
102B ARG 3.2 10.5 - - - +
103B ASP* 1.3 90.2 - - - +
105B ARG* 1.3 61.4 + - - +
107B ILE* 3.5 4.7 + - + +
108B ALA 3.1 16.6 + - - -
366B ASN* 3.8 19.5 - - - +
368B TYR* 3.3 24.2 - - + +
369B LEU* 3.8 22.8 - - + +
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Residues in contact with ARG 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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21B PHE* 6.5 0.2 - - - +
22B THR* 5.9 2.9 - - - +
70B ASP* 3.1 34.5 + - - +
73B THR* 3.5 13.7 - - - +
88B ARG* 3.8 13.7 - - - +
89B CYS 3.8 16.5 + - - +
90B ASP* 3.0 34.6 + - - +
103B ASP* 2.9 11.9 + - - +
104B PRO* 1.3 76.6 - - - +
106B SER* 1.3 66.4 + - - +
108B ALA* 3.2 3.6 + - - +
109B LYS* 3.1 33.6 + - + +
229B THR* 4.3 10.3 - - + +
233B ASP* 2.9 37.4 + - - -
368B TYR* 3.9 27.9 - - + -
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Residues in contact with SER 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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90B ASP* 4.4 9.9 + - - +
91B ILE 3.9 8.1 + - - -
92B LEU* 4.6 1.2 - - - +
99B GLY* 3.9 14.8 - - - -
100B TYR 3.9 13.5 - - - -
103B ASP* 2.9 29.7 + - - -
105B ARG* 1.3 77.4 - - - +
107B ILE* 1.3 59.6 + - - +
109B LYS* 3.1 13.2 + - - +
110B ARG* 2.9 39.2 + - - +
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Residues in contact with ILE 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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100B TYR 5.1 0.9 - - - +
101B ASP 3.5 24.2 - - - +
102B ARG 4.7 3.6 - - - +
103B ASP 3.0 18.4 + - - +
104B PRO* 3.5 9.4 - - + +
106B SER* 1.3 77.0 - - - +
108B ALA* 1.3 61.8 + - - +
110B ARG* 3.4 12.8 + - - +
111B ALA* 3.1 18.4 + - - +
369B LEU* 3.8 22.0 - - + -
372B ALA* 4.5 5.2 - - + -
433B VAL* 3.6 20.1 - - + +
434B PHE* 3.7 45.5 - - + -
438B ALA* 4.7 7.2 - - + -
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Residues in contact with ALA 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 PRO 3.1 13.8 + - - +
105B ARG 3.2 7.6 + - - +
107B ILE* 1.3 76.3 - - - +
109B LYS* 1.3 63.6 + - - +
111B ALA 3.3 1.4 + - - -
112B GLU* 3.1 19.1 + - - +
228B MET* 3.3 26.5 - - + +
229B THR* 3.5 15.7 - - + +
232B ALA* 5.8 0.2 - - + -
368B TYR* 4.0 28.9 - - + +
372B ALA* 4.4 5.8 - - - -
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Residues in contact with LYS 109 (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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70B ASP* 3.8 9.7 + - - -
90B ASP* 3.1 39.2 + - - +
105B ARG* 3.1 34.0 + - - +
106B SER* 3.4 11.7 - - - +
108B ALA* 1.3 74.9 - - - +
110B ARG* 1.3 59.8 + - + +
112B GLU* 3.0 7.6 + - - +
113B ASP* 2.9 36.8 + - - +
229B THR* 4.0 18.6 - - + +
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Residues in contact with ARG 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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98B GLN* 3.7 16.0 - - - +
99B GLY* 2.8 29.7 + - - -
100B TYR 3.9 2.2 + - - -
101B ASP* 2.9 37.2 + - - +
106B SER* 2.9 23.0 + - - +
107B ILE* 3.6 9.9 - - - +
109B LYS* 1.3 77.3 - - - +
111B ALA* 1.3 56.3 + - - +
113B ASP* 3.5 11.5 + - - +
114B TYR* 2.9 30.3 + - - +
431B GLY 5.5 2.1 - - - +
432B GLY 3.2 18.5 + - - -
433B VAL* 3.1 38.4 + - + +
435B THR* 4.0 7.7 - - - +
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Residues in contact with ALA 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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107B ILE 3.1 13.4 + - - +
108B ALA 3.6 8.7 - - - +
109B LYS 3.2 0.2 - - - -
110B ARG* 1.3 74.8 - - - +
112B GLU* 1.3 64.9 + - - +
114B TYR* 3.6 5.6 + - - +
115B LEU 3.2 15.8 + - - -
228B MET* 4.1 12.6 - - + -
372B ALA* 4.2 10.1 - - + -
375B LEU* 3.7 18.4 - - + +
376B MET* 4.1 13.2 - - + -
433B VAL* 4.0 19.0 - - + +
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Residues in contact with GLU 112 (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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108B ALA 3.1 16.7 + - - +
109B LYS* 3.0 9.9 + - - +
111B ALA* 1.3 73.0 - - - +
113B ASP* 1.3 67.5 + - - +
115B LEU* 3.2 20.9 + - - +
116B ARG* 3.4 31.4 + - - +
122B ASP 5.2 0.2 - - - +
123B THR* 5.1 1.9 - - - +
124B VAL* 3.4 29.1 + - + +
227B THR* 4.2 11.8 + - - -
228B MET* 3.8 21.0 + - + -
229B THR* 3.1 37.2 + - - +
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Residues in contact with ASP 113 (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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109B LYS* 2.9 19.7 + - - +
110B ARG* 3.5 14.9 - - - +
112B GLU* 1.3 76.5 - - - +
114B TYR* 1.3 58.2 + - - +
116B ARG* 3.0 31.9 + - - +
117B ALA* 2.8 27.7 + - - +
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Residues in contact with TYR 114 (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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110B ARG 2.9 18.4 + - - +
111B ALA 3.9 3.8 - - - +
113B ASP* 1.3 73.2 - - - +
115B LEU* 1.3 65.2 + - - +
117B ALA* 3.7 10.7 - - + +
118B THR* 3.1 42.0 + - + +
376B MET* 4.1 18.2 - - + -
379B LEU* 3.7 32.5 - - + -
383B LYS* 3.3 33.1 + - - +
430B ALA* 3.7 13.3 - - + +
431B GLY* 3.4 37.7 - - - +
433B VAL* 4.3 9.2 - - + -
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Residues in contact with LEU 115 (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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111B ALA 3.2 12.1 + - - +
112B GLU* 3.2 14.0 + - - +
113B ASP 3.1 1.0 - - - -
114B TYR* 1.3 76.0 - - - +
116B ARG* 1.3 61.9 + - - +
118B THR* 2.9 20.6 + - - -
119B GLY 3.4 2.9 + - - -
120B ILE* 3.8 6.5 + - + -
121B ALA* 3.3 47.9 - - + +
122B ASP 4.2 2.0 - - - +
123B THR 3.9 12.3 - - - +
124B VAL* 3.7 26.0 - - + -
274B LEU* 3.9 12.3 - - + -
375B LEU* 4.4 3.4 - - + -
379B LEU* 3.4 38.8 - - + -
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Residues in contact with ARG 116 (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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112B GLU* 3.4 26.6 + - - +
113B ASP* 3.0 41.5 + - - +
115B LEU* 1.3 78.3 - - - +
117B ALA* 1.3 59.5 + - - +
119B GLY* 2.8 22.0 + - - -
121B ALA 3.5 5.8 - - - +
122B ASP* 3.3 48.8 + - + +
123B THR* 5.0 4.9 - - - +
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Residues in contact with ALA 117 (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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113B ASP 2.8 16.1 + - - +
114B TYR* 3.7 14.1 - - + +
115B LEU 3.4 0.4 - - - -
116B ARG* 1.3 77.1 - - - +
118B THR* 1.3 62.0 + - + +
119B GLY* 3.3 0.9 + - - -
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Residues in contact with THR 118 (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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114B TYR* 3.1 47.9 + - + +
115B LEU* 2.9 17.5 + - - +
117B ALA* 1.3 76.2 - - + +
119B GLY* 1.3 56.5 + - - +
120B ILE* 3.0 38.1 + - + +
379B LEU* 5.0 0.5 - - - +
383B LYS* 5.0 8.5 - - + -
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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