Contacts of the helix formed by residues 104 - 111 (chain A) in PDB entry 3F7H
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 PRO 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A THR 3.6 10.3 - - - +
101A ALA 4.9 3.6 - - - +
102A GLU 4.3 3.8 - - - +
103A VAL* 1.3 87.1 - - + +
105A PRO* 1.3 71.4 - - + +
106A GLU* 3.9 15.3 - - + +
107A LEU* 3.1 40.5 + - + +
108A LEU* 3.1 13.3 + - - +
138A ASP 5.3 3.8 - - - +
140A PRO* 5.8 0.4 - - + -
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Residues in contact with PRO 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.7 12.7 - - + +
94A PHE* 3.6 31.0 - - + +
97A TRP* 3.7 23.3 - - + -
100A THR* 4.1 22.9 - - + +
103A VAL 3.4 6.0 - - - +
104A PRO* 1.3 82.8 - - + +
106A GLU* 1.3 67.1 + - - +
108A LEU* 3.3 12.1 + - + +
109A ALA* 2.9 33.8 + - - +
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Residues in contact with GLU 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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87A GLU* 4.4 3.1 - - - +
91A LEU* 3.9 26.9 - - + +
100A THR* 5.8 0.9 - - - +
104A PRO* 3.9 10.5 - - + +
105A PRO* 1.3 88.3 - - - +
107A LEU* 1.3 62.6 + - + +
109A ALA* 4.0 1.8 - - - +
110A ALA* 3.1 27.9 + - - +
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Residues in contact with LEU 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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104A PRO* 3.1 34.1 + - + +
106A GLU* 1.3 79.6 - - + +
108A LEU* 1.3 64.4 + - - +
110A ALA* 3.5 9.2 + - + +
111A ALA* 3.0 26.0 + - - +
138A ASP 6.1 0.2 - - - +
139A ASP* 6.2 2.2 - - - +
140A PRO* 3.7 24.0 - - + +
141A TRP* 5.5 6.7 + - + -
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Residues in contact with LEU 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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94A PHE* 3.6 24.9 - - + -
97A TRP* 3.4 37.0 - - + +
103A VAL* 3.8 23.3 - - + +
104A PRO 3.1 13.4 + - - +
105A PRO* 3.7 4.0 - - + +
107A LEU* 1.3 76.0 - - - +
109A ALA* 1.3 62.6 + - - +
111A ALA 3.2 7.3 + - - -
112A GLY 3.4 0.3 + - - -
113A PHE* 3.0 35.1 + - + +
122A VAL* 4.7 3.8 - - + -
134A TRP* 3.6 39.3 - - + -
140A PRO* 3.8 13.0 - - + +
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Residues in contact with ALA 109 (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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87A GLU* 4.0 12.6 - - + +
90A ARG* 2.9 34.9 + - + -
91A LEU* 3.6 37.2 - - + +
94A PHE* 4.1 1.5 - - + -
105A PRO 2.9 20.7 + - - +
106A GLU 4.0 3.1 - - - +
108A LEU* 1.3 71.0 - - - +
110A ALA* 1.3 64.1 + - - +
112A GLY 3.1 2.4 + - - -
113A PHE 3.5 11.8 + - - -
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Residues in contact with ALA 110 (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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87A GLU* 3.5 25.0 + - - +
90A ARG* 4.2 1.4 + - - -
106A GLU 3.1 19.5 + - - +
107A LEU* 3.8 12.6 - - + +
108A LEU 3.3 0.2 - - - -
109A ALA* 1.3 76.4 - - - +
111A ALA* 1.3 57.5 + - - +
112A GLY 3.2 3.5 + - - -
141A TRP* 3.3 24.0 - - + +
153A PHE* 4.0 9.4 - - - -
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Residues in contact with ALA 111 (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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107A LEU 3.0 18.0 + - - +
108A LEU 3.7 4.7 - - - +
109A ALA 3.1 0.8 - - - -
110A ALA* 1.3 76.1 - - - +
112A GLY* 1.3 55.7 + - - +
113A PHE* 3.5 10.6 + - + -
140A PRO* 3.7 19.3 - - + -
141A TRP* 3.6 34.3 - - + +
144A HIS* 2.7 32.7 + - - -
153A PHE* 3.8 5.3 - - - -
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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