Contacts of the helix formed by residues 102 - 113 (chain A) in PDB entry 3M5B
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 VAL 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TYR* 5.5 0.2 - - + -
50A VAL* 3.2 33.4 - - + -
51A SER* 4.5 0.9 - - - -
54A LEU* 4.2 25.6 - - + -
74A LEU* 4.3 23.8 - - + -
77A PHE* 5.0 2.5 - - + -
78A VAL* 4.3 11.2 - - + -
97A ALA* 2.9 19.5 + - + +
100A LEU* 4.2 5.8 - - + +
101A GLY* 1.3 68.9 - - - -
103A GLN* 1.3 64.2 + - - +
104A SER* 4.0 9.0 - - - +
105A LEU* 3.2 22.7 + - + +
106A GLU* 3.1 19.0 + - - +
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Residues in contact with GLN 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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50A VAL 4.8 2.6 + - - -
101A GLY 3.3 7.7 + - - +
102A VAL* 1.3 73.8 - - - +
104A SER* 1.3 63.1 + - - +
106A GLU* 3.3 15.0 + - - +
107A GLU* 3.2 26.0 + - + +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 4.4 17.5 - - - -
12A TYR* 2.9 34.3 + - - -
77A PHE* 3.8 7.6 - - - -
102A VAL* 4.0 6.4 - - - +
103A GLN* 1.3 77.8 - - - +
105A LEU* 1.3 60.9 + - - +
107A GLU* 3.8 3.8 + - - +
108A ALA* 3.2 22.7 + - - +
111A ARG* 5.2 1.4 + - - -
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Residues in contact with LEU 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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8A LEU* 3.9 12.1 - - + -
74A LEU* 4.0 25.8 - - + +
77A PHE* 3.8 34.5 - - + -
93A LEU* 3.7 37.0 - - + +
97A ALA* 3.8 18.4 - - + -
102A VAL* 3.2 18.5 + - + +
104A SER* 1.3 78.6 + - - +
106A GLU* 1.3 68.2 + - - +
108A ALA* 4.4 1.1 - - + -
109A CYS* 3.0 38.8 + - - -
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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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94A GLN* 3.9 30.1 + - + +
97A ALA* 3.7 12.6 - - + +
98A ARG* 3.5 41.4 - - - +
102A VAL 3.1 13.1 + - - +
103A GLN* 3.3 17.8 + - - +
105A LEU* 1.3 77.2 - - - +
107A GLU* 1.3 57.3 + - - +
109A CYS* 3.4 4.0 + - - +
110A TRP* 3.2 26.3 + - + +
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Residues in contact with GLU 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 GLN* 3.2 18.0 + - + +
104A SER* 4.2 4.3 - - - +
106A GLU* 1.3 74.9 - - - +
108A ALA* 1.3 65.3 + - - +
110A TRP* 3.0 35.9 + - - +
111A ARG* 2.9 56.8 + - - +
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Residues in contact with ALA 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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8A LEU* 3.9 21.5 - - + +
9A PRO* 5.1 6.7 - - + +
77A PHE* 4.6 12.3 - - + -
104A SER 3.2 19.3 + - - +
105A LEU* 3.4 8.3 + - + +
107A GLU* 1.3 76.2 - - - +
109A CYS* 1.3 62.6 + - - +
111A ARG* 3.5 20.1 + - - +
112A ALA* 3.1 23.4 + - - +
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Residues in contact with CYS 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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8A LEU* 3.9 13.0 - - - -
90A LEU* 3.8 23.0 - - + +
93A LEU* 4.0 11.4 - - - -
94A GLN* 3.7 43.5 - - + +
105A LEU* 3.0 38.6 + - - +
106A GLU 3.7 1.6 - - - +
108A ALA* 1.3 76.2 - - - +
110A TRP* 1.3 62.8 + - - +
112A ALA* 3.3 2.9 + - - -
113A ARG* 3.2 22.7 + - - +
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Residues in contact with TRP 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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94A GLN* 3.7 26.2 + - - +
106A GLU* 3.2 13.8 + - + +
107A GLU* 3.0 38.1 - - - +
109A CYS* 1.3 78.1 - - - +
111A ARG* 1.3 66.0 + - + +
113A ARG* 3.4 29.3 + - + +
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Residues in contact with ARG 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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104A SER 5.2 1.0 + - - -
107A GLU* 2.9 48.1 + - - +
108A ALA* 3.5 33.9 - - - +
110A TRP* 1.3 83.9 - - + +
112A ALA* 1.3 60.9 + - - +
113A ARG 3.3 4.0 + - - +
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Residues in contact with ALA 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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6A ILE* 3.8 31.2 - - + +
7A ARG 5.7 0.4 - - - +
8A LEU* 4.0 11.0 - - + -
90A LEU* 3.9 10.8 - - + +
108A ALA 3.1 13.9 + - - +
109A CYS 3.3 5.1 + - - +
111A ARG* 1.3 77.6 - - - +
113A ARG* 1.3 63.7 + - - +
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Residues in contact with ARG 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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90A LEU* 3.9 22.9 - - + +
91A ARG* 3.7 44.5 - - - +
94A GLN* 3.1 38.5 + - - +
109A CYS 3.2 9.3 + - - +
110A TRP* 3.6 28.4 - - + +
111A ARG 3.2 5.8 - - - +
112A ALA* 1.3 83.6 - - - +
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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