Contacts of the helix formed by residues 103 - 118 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H PHE* 6.0 0.7 - - - +
22H THR 4.7 3.3 + - - +
57H TRP* 4.4 4.0 - - - -
89H CYS 5.6 0.4 - - - +
90H ASP* 3.7 5.6 - - - -
91H ILE* 2.8 43.0 + - + +
100H TYR* 3.1 29.2 + - + +
102H ARG* 1.3 74.2 - - - +
104H PRO* 1.3 73.4 - - - +
105H ARG* 2.9 18.1 + - - +
106H SER* 2.9 23.8 + - - +
107H ILE* 3.0 24.0 + - - +
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Residues in contact with PRO 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H THR* 3.6 16.2 - - + +
23H ASP 3.5 24.7 - - - +
24H THR* 4.1 4.7 - - - +
57H TRP* 3.9 5.2 - - + -
102H ARG 3.2 10.9 - - - +
103H ASP* 1.3 89.2 - - - +
105H ARG* 1.3 60.2 + - - +
107H ILE* 3.5 5.1 + - + +
108H ALA 3.1 17.0 + - - -
366H ASN* 3.8 18.8 - - - +
368H TYR* 3.3 25.3 - - + +
369H LEU* 3.8 22.6 - - + +
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Residues in contact with ARG 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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21H PHE* 6.5 0.2 - - - +
22H THR* 5.9 2.7 - - - +
70H ASP* 3.1 33.7 + - - +
73H THR* 3.5 13.3 - - - +
88H ARG* 3.8 14.2 - - - +
89H CYS 3.8 15.4 + - - +
90H ASP* 3.0 34.0 + - - +
103H ASP* 2.9 11.7 + - - +
104H PRO* 1.3 76.5 - - - +
106H SER* 1.3 67.0 + - - +
108H ALA* 3.2 3.6 + - - +
109H LYS* 3.1 33.8 + - + +
229H THR* 4.3 9.7 - - + +
233H ASP* 2.9 37.7 + - - -
368H TYR* 3.9 27.9 - - + -
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Residues in contact with SER 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ASP* 4.4 9.1 + - - +
91H ILE 3.9 8.3 + - - -
92H LEU* 4.6 1.0 - - - +
99H GLY* 3.9 14.7 - - - -
100H TYR 3.9 13.5 - - - -
103H ASP* 2.9 31.3 + - - -
105H ARG* 1.3 77.1 - - - +
107H ILE* 1.3 57.2 + - - +
109H LYS* 3.1 13.2 + - - +
110H ARG* 2.9 40.2 + - - +
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Residues in contact with ILE 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H TYR 5.1 0.7 - - - +
101H ASP 3.5 24.9 - - - +
102H ARG 4.7 3.4 - - - -
103H ASP 3.0 18.8 + - - +
104H PRO* 3.5 9.9 - - + +
105H ARG 3.2 0.2 - - - -
106H SER* 1.3 76.1 - - - +
108H ALA* 1.3 61.3 + - - +
110H ARG* 3.3 13.8 + - - +
111H ALA* 3.1 18.0 + - - +
369H LEU* 3.8 21.8 - - + -
372H ALA* 4.5 4.7 - - + -
433H VAL* 3.6 19.3 - - + +
434H PHE* 3.7 46.9 - - + -
438H ALA* 4.7 7.2 - - + -
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Residues in contact with ALA 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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104H PRO 3.1 13.6 + - - +
105H ARG 3.2 7.8 + - - +
107H ILE* 1.3 76.1 - - - +
109H LYS* 1.3 62.1 + - - +
111H ALA 3.3 1.2 + - - -
112H GLU* 3.1 19.8 + - - +
228H MET* 3.3 25.9 - - + +
229H THR* 3.5 16.4 - - + +
232H ALA* 5.8 0.2 - - + -
368H TYR* 4.0 28.9 - - + +
372H ALA* 4.4 5.4 - - - -
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Residues in contact with LYS 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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70H ASP* 3.8 9.8 + - - -
90H ASP* 3.1 38.4 + - - +
105H ARG* 3.1 33.4 + - - +
106H SER* 3.4 12.3 - - - +
108H ALA* 1.3 74.9 - - - +
110H ARG* 1.3 59.0 + - - +
112H GLU* 3.0 7.2 + - - +
113H ASP* 2.9 36.5 + - - +
229H THR* 4.0 18.8 - - + +
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Residues in contact with ARG 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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98H GLN* 3.7 15.4 - - - +
99H GLY* 2.8 29.1 + - - -
100H TYR 3.9 2.4 + - - -
101H ASP* 2.9 36.4 + - - +
106H SER* 2.9 23.5 + - - +
107H ILE* 3.6 11.0 - - - +
109H LYS* 1.3 75.0 - - - +
111H ALA* 1.3 59.2 + - - +
113H ASP* 3.5 11.7 - - - +
114H TYR* 2.9 30.5 + - - +
431H GLY 5.5 2.1 - - - +
432H GLY 3.2 18.1 + - - -
433H VAL* 3.1 38.4 + - + +
435H THR* 4.0 7.7 - - - +
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Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H ILE 3.1 13.8 + - - +
108H ALA 3.6 9.4 - - - +
109H LYS 3.2 0.2 - - - -
110H ARG* 1.3 74.4 - - - +
112H GLU* 1.3 63.9 + - - +
114H TYR* 3.9 4.5 - - - +
115H LEU* 3.2 16.1 + - - +
228H MET* 4.1 12.8 - - + -
372H ALA* 4.2 10.3 - - + -
375H LEU* 3.7 18.2 - - + +
376H MET* 4.1 14.5 - - + +
433H VAL* 4.0 19.7 - - + +
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Residues in contact with GLU 112 (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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108H ALA 3.1 18.0 + - - +
109H LYS* 3.0 10.3 + - - +
111H ALA* 1.3 72.8 - - - +
113H ASP* 1.3 66.1 + - - +
115H LEU* 3.2 20.2 + - - +
116H ARG* 3.4 31.6 + - - +
123H THR* 5.1 2.1 - - - +
124H VAL* 3.4 28.8 + - + +
227H THR* 4.2 11.8 + - - -
228H MET* 3.8 20.3 + - + -
229H THR* 3.1 39.1 + - - +
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Residues in contact with ASP 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H LYS* 2.9 20.8 + - - +
110H ARG* 3.5 15.5 - - - +
112H GLU* 1.3 76.0 - - - +
114H TYR* 1.3 58.3 + - - +
116H ARG* 3.0 31.3 + - - +
117H ALA* 2.8 27.8 + - - +
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Residues in contact with TYR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H ARG 2.9 17.3 + - - +
111H ALA 3.9 3.6 - - - +
112H GLU 3.4 0.2 - - - -
113H ASP* 1.3 73.4 - - - +
115H LEU* 1.3 65.4 + - - +
117H ALA* 3.7 10.7 - - + +
118H THR* 3.1 41.1 + - + +
376H MET* 4.1 17.5 - - + -
379H LEU* 3.7 32.8 - - + -
383H LYS* 3.3 33.8 + - + +
430H ALA* 3.7 12.8 - - + +
431H GLY* 3.4 37.7 - - - +
433H VAL* 4.3 9.4 - - + -
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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
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111H ALA 3.2 12.5 + - - +
112H GLU* 3.2 13.4 + - - +
113H ASP 3.1 0.8 - - - -
114H TYR* 1.3 74.5 - - - +
116H ARG* 1.3 62.0 + - + +
118H THR* 2.9 20.2 + - - +
119H GLY 3.4 3.1 + - - -
120H ILE* 3.8 5.4 + - + -
121H ALA* 3.3 48.7 - - + +
122H ASP 4.2 2.0 - - - +
123H THR 3.9 12.1 - - - +
124H VAL* 3.7 25.6 - - + -
274H LEU* 3.9 13.0 - - + -
375H LEU* 4.4 3.4 - - + -
379H LEU* 3.4 38.4 - - + -
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Residues in contact with ARG 116 (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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112H GLU* 3.4 26.6 + - - +
113H ASP* 3.0 42.2 + - - +
115H LEU* 1.3 77.6 - - - +
117H ALA* 1.3 60.2 + - - +
119H GLY* 2.8 21.7 + - - -
121H ALA 3.5 5.2 - - - -
122H ASP* 3.3 48.1 + - + +
123H THR* 5.0 4.9 - - - +
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H ASP 2.8 16.7 + - - +
114H TYR* 3.7 13.9 - - + +
115H LEU 3.4 0.2 - - - -
116H ARG* 1.3 76.2 - - - +
118H THR* 1.3 61.1 + - + +
119H GLY* 3.3 1.0 + - - -
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Residues in contact with THR 118 (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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114H TYR* 3.1 46.5 + - + +
115H LEU* 2.9 18.0 + - - +
117H ALA* 1.3 76.2 - - + +
119H GLY* 1.3 57.3 + - - +
120H ILE* 3.0 37.7 + - + +
379H LEU* 5.0 0.3 - - - +
383H LYS* 5.0 9.0 - - + -
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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