Contacts of the helix formed by residues 99 - 108 (chain A) in PDB entry 1FO4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.3 34.9 + - + +
97A ARG 3.7 1.6 + - - -
98A LEU* 1.3 73.0 - - - +
100A PRO* 1.3 78.3 - - + +
101A VAL* 3.1 40.0 + - + +
102A GLN* 2.8 27.7 + - + +
103A GLU* 2.9 10.7 + - - +
125A TYR* 3.4 16.9 - + - -
128A LEU* 4.8 2.0 - - + -
202A MET* 5.2 0.2 - - - -
204A LEU* 3.6 25.6 - - + +
209A GLU* 3.2 39.7 + - - -
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Residues in contact with PRO 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU 3.8 0.2 - - - -
99A HIS* 1.3 98.8 - - + +
101A VAL* 1.3 56.1 + - - +
103A GLU* 3.2 11.6 + - + +
104A ARG* 2.9 37.8 + - - +
163A PHE* 3.9 22.9 - - + -
202A MET* 3.7 47.3 - - + +
203A PRO 4.0 8.7 - - - +
204A LEU* 4.1 13.0 - - + -
205A ASP 5.4 0.2 - - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 5.1 1.6 - - + -
99A HIS* 3.1 19.5 + - + +
100A PRO* 1.3 75.8 - - - +
102A GLN* 1.3 62.3 + - + +
105A ILE* 3.2 21.0 + - - +
121A VAL* 3.5 41.1 - - + +
124A MET* 3.9 8.1 - - + -
125A TYR* 4.3 9.6 - - - +
128A LEU* 3.4 33.7 - - + -
160A PHE* 3.5 19.7 - - + -
163A PHE* 4.0 11.7 - - + -
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 3.3 28.1 + - - +
91A ILE* 3.7 14.0 - - + +
92A GLY* 3.3 20.8 + - - -
98A LEU* 3.5 14.2 - - + +
99A HIS 2.8 33.2 + - - +
101A VAL* 1.3 70.4 - - - +
103A GLU* 1.3 66.7 + - - +
105A ILE* 3.3 5.9 - - - +
106A ALA* 3.3 24.1 + - - +
121A VAL* 3.9 13.2 - - + -
586A ALA* 3.2 37.9 + - + +
587A SER* 3.3 13.4 - - - +
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.2 23.5 - - + +
99A HIS 2.9 12.2 + - - +
100A PRO* 3.7 10.7 - - + +
102A GLN* 1.3 78.3 - - - +
104A ARG* 1.3 59.0 + - - +
106A ALA* 3.8 1.8 - - - +
107A LYS* 3.0 64.7 + - + +
200A GLU 4.3 4.9 - - - +
201A PHE* 3.7 11.2 - - + +
202A MET* 3.0 39.4 + - - +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PRO* 2.9 17.6 + - - +
101A VAL 4.2 2.0 - - - +
103A GLU* 1.3 77.7 + - - +
105A ILE* 1.3 65.0 + - - +
108A SER* 2.9 31.3 + - - -
159A GLY* 4.4 8.1 - - - +
160A PHE* 4.6 8.3 - - + -
162A THR* 2.9 43.3 + - - -
163A PHE* 3.4 44.5 - - + -
201A PHE* 3.4 43.7 - - + +
202A MET 3.0 28.9 + - - -
203A PRO* 4.0 9.1 - - - +
204A LEU 4.1 3.4 - - - +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL 3.2 14.1 + - - +
102A GLN 3.3 12.3 - - - +
104A ARG* 1.3 78.4 - - - +
106A ALA* 1.3 63.4 + - - +
108A SER* 4.7 2.7 - - - -
109A HIS 3.7 0.2 + - - -
110A GLY* 2.8 57.1 + - - +
111A SER* 4.6 0.9 - - - +
117A THR* 4.0 21.5 - - + -
120A ILE* 3.8 29.8 - - + -
121A VAL* 4.1 7.4 - - + -
156A ILE* 4.1 12.8 - - + +
159A GLY* 6.0 0.7 - - - -
160A PHE* 3.7 19.0 - - + -
586A ALA* 3.7 19.1 - - + -
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 5.5 0.9 - - + -
102A GLN 3.3 15.0 + - - +
103A GLU* 3.8 4.3 - - - +
104A ARG 3.1 0.4 - - - -
105A ILE* 1.3 83.9 - - - +
107A LYS* 1.3 64.8 + - + +
109A HIS* 3.4 11.1 + - - -
111A SER* 5.0 2.4 + - - -
578A PRO* 3.9 14.9 - - - +
582A ALA* 3.8 43.3 - - + +
583A ALA* 3.9 11.0 - - + +
586A ALA* 4.4 1.8 - - + -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 3.0 51.0 + - + +
106A ALA* 1.3 77.9 - - + +
108A SER* 1.3 58.7 + - - +
109A HIS* 3.2 13.7 + - - -
196A PHE* 3.2 20.5 - - + +
200A GLU* 3.0 32.9 + - - +
201A PHE* 3.9 20.9 - - + -
578A PRO* 4.7 13.7 - - + +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG 2.9 21.3 + - - -
105A ILE* 4.3 4.3 - - - -
106A ALA 3.2 0.4 - - - -
107A LYS* 1.3 75.1 - - - +
109A HIS* 1.3 77.1 + - - +
110A GLY 3.4 0.8 + - - -
154A ARG* 4.4 4.9 + - - -
155A PRO* 3.4 21.2 - - - +
159A GLY* 3.2 30.8 - - - -
196A PHE* 3.6 28.5 - - - -
201A PHE* 3.9 3.6 - - - -
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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