Contacts of the helix formed by residues 108 - 118 (chain A) in PDB entry 3Q02
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 GLY 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.2 0.8 + - - -
107A GLN* 1.3 85.3 + - - +
109A PHE* 1.3 62.6 + - - +
110A MET 4.9 0.2 - - - +
111A PRO* 3.3 30.3 - - - +
112A HIS* 3.4 15.2 - - - +
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Residues in contact with PHE 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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48A LEU* 3.7 22.2 - - + -
49A THR* 3.4 35.9 - - + -
105A LEU* 5.5 1.8 - - + -
106A VAL* 3.1 22.8 + - + +
107A GLN 3.3 1.2 + - - -
108A GLY* 1.3 75.2 - - - +
110A MET* 1.3 76.2 + - + +
112A HIS* 2.9 9.2 + + + +
113A PHE* 2.8 53.9 + + + -
121A VAL* 3.6 24.5 - - + -
308A SER* 3.3 27.1 - - - +
309A LEU* 3.7 19.3 - - + +
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Residues in contact with MET 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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105A LEU* 4.2 24.9 - - + -
106A VAL 4.7 0.8 + - - +
109A PHE* 1.3 94.8 - - + +
111A PRO* 1.3 69.7 - - + +
113A PHE* 3.8 2.2 - - + +
114A PHE* 2.9 26.4 + - - +
120A THR* 3.4 39.5 - - + -
121A VAL* 3.6 30.3 - - + +
123A GLN* 5.5 2.9 - - - +
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Residues in contact with PRO 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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108A GLY* 3.3 31.6 - - - +
110A MET* 1.3 94.6 - - + +
112A HIS* 1.3 54.2 + - - -
114A PHE* 4.1 6.0 - - + +
115A ARG* 3.1 28.2 + - - +
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Residues in contact with HIS 112 (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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48A LEU* 4.1 20.6 - - + -
67A ASP* 3.3 29.1 + - - -
108A GLY 3.4 16.9 + - - +
109A PHE* 2.9 8.1 + + - +
111A PRO* 1.3 78.3 - - - +
113A PHE* 1.3 66.4 + - - +
115A ARG* 3.1 38.2 + - - +
116A LEU* 3.1 42.2 + - + +
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Residues in contact with PHE 113 (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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45A MET* 4.0 40.4 - - + -
48A LEU* 4.2 16.1 - - + +
49A THR* 4.7 0.2 - - + -
97A ILE* 4.1 11.2 - - + -
109A PHE* 2.8 50.8 + + + +
110A MET* 3.8 5.6 - - + +
112A HIS* 1.3 74.1 - - - +
114A PHE* 1.3 56.9 + - - +
116A LEU 3.4 0.2 + - - -
117A PHE* 2.9 47.2 + + - +
119A SER* 3.2 42.6 - - - -
120A THR* 3.9 16.4 - - - -
121A VAL* 4.1 14.8 - - + -
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Residues in contact with PHE 114 (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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110A MET 2.9 18.5 + - - +
111A PRO* 4.1 5.6 - - + +
113A PHE* 1.3 76.0 - - - +
115A ARG* 1.3 63.3 + - - +
118A ARG* 2.8 67.1 + - + -
119A SER* 3.3 24.6 + - - +
120A THR* 3.9 14.8 - - + -
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Residues in contact with ARG 115 (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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76A ARG* 3.5 3.7 + - - +
111A PRO 3.1 18.6 + - - +
112A HIS* 3.1 38.4 + - - +
114A PHE* 1.3 79.1 - - - +
116A LEU* 1.3 76.9 + - + +
118A ARG* 2.9 33.8 + - - +
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Residues in contact with LEU 116 (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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48A LEU* 3.6 24.2 - - + -
66A ILE* 4.6 6.5 - - + +
67A ASP* 4.0 12.8 - - - +
72A ALA* 3.6 30.1 - - + +
76A ARG* 2.9 32.1 + - - +
112A HIS* 3.1 36.5 + - + +
113A PHE 4.0 2.7 - - - +
115A ARG* 1.3 107.6 - - + +
117A PHE* 1.3 72.2 + - + +
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Residues in contact with PHE 117 (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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41A SER* 4.9 1.6 - - - -
44A ALA* 3.7 10.5 - - + -
45A MET* 3.5 54.7 - - + +
48A LEU* 3.1 28.5 - - + -
66A ILE* 3.9 26.5 - - + -
72A ALA* 5.4 2.0 - - + -
75A LEU* 5.0 10.1 - - + -
76A ARG* 4.8 5.6 - - + +
113A PHE* 2.9 33.7 + + + +
116A LEU* 1.3 82.6 - - + +
118A ARG* 1.3 76.9 + - - +
119A SER* 3.1 16.8 + - - +
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Residues in contact with ARG 118 (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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76A ARG* 3.2 42.1 - - - +
80A LYS* 5.9 3.4 - - - +
114A PHE* 2.8 57.1 + - + -
115A ARG* 2.9 25.6 + - - +
117A PHE* 1.3 81.9 - - - +
119A SER* 1.3 58.8 + - - +
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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