Contacts of the helix formed by residues 101 - 110 (chain A) in PDB entry 3EXF
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 SER 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 4.9 2.9 - - - -
99A GLY 3.7 2.8 + - - -
100A LEU* 1.3 74.8 - - - +
102A VAL* 1.3 67.6 + - - +
103A ARG* 3.8 11.3 - - - +
104A GLU* 3.2 42.4 + - - +
105A ILE* 3.2 12.7 + - - +
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Residues in contact with VAL 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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41A THR* 3.6 31.2 - - + -
45A MET* 3.7 23.3 - - + -
96A PHE* 3.8 14.9 - - + -
101A SER* 1.3 72.8 - - - +
103A ARG* 1.3 65.1 + - - +
104A GLU 2.9 0.9 + - - -
105A ILE* 3.0 4.5 + - - -
106A LEU* 2.9 51.2 + - + +
316A GLU* 5.0 6.7 - - + +
317A ILE* 4.0 16.8 - - + -
320A ALA* 3.8 11.2 - - + -
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Residues in contact with ARG 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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101A SER* 3.8 11.0 - - - +
102A VAL* 1.3 75.7 - - - +
104A GLU* 1.3 57.4 + - + +
106A LEU* 4.4 0.7 - - - +
107A ALA* 3.0 31.5 + - - +
316A GLU* 4.3 6.1 + - - +
319A ASP* 3.0 37.8 + - - +
320A ALA* 3.5 26.4 - - - +
323A PHE* 3.5 47.6 - - + +
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Residues in contact with GLU 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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99A GLY 4.5 1.6 - - - +
100A LEU* 3.5 29.9 - - + +
101A SER* 3.2 30.4 + - - +
102A VAL 3.1 1.0 - - - -
103A ARG* 1.3 78.4 - - + +
105A ILE* 1.3 68.4 + - - +
108A GLU* 3.4 8.3 + - - +
114A GLY 4.4 16.2 - - - +
115A GLY* 3.6 0.9 - - - -
116A CYS* 3.2 44.7 + - + +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A MET* 3.7 31.9 - - + -
92A HIS* 3.9 14.1 - - + +
95A THR* 3.7 21.8 - - + -
96A PHE* 3.6 44.0 - - + +
100A LEU* 4.0 5.6 - - + +
101A SER 3.2 13.8 + - - +
102A VAL 3.0 4.6 + - - +
104A GLU* 1.3 75.7 - - - +
106A LEU* 1.3 69.7 + - - +
108A GLU* 2.9 16.1 + - - +
109A LEU* 3.1 17.9 + - + +
116A CYS* 5.0 1.1 - - - -
126A MET* 4.2 19.7 - - - -
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Residues in contact with LEU 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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45A MET* 4.2 14.8 - - + +
48A LYS* 4.0 16.8 - - + -
49A ALA* 4.2 26.0 - - + +
52A LEU* 4.2 16.6 - - + -
58A ILE* 5.4 0.2 - - + -
102A VAL* 2.9 42.7 + - + +
103A ARG 4.4 0.2 - - - +
105A ILE* 1.3 71.7 - - - +
107A ALA* 1.3 59.4 + - - +
109A LEU* 3.2 15.0 + - + +
110A THR* 2.9 27.5 + - - +
317A ILE* 4.7 2.7 - - + +
320A ALA* 3.8 4.9 - - + +
321A ALA* 3.8 24.5 - - - +
324A ALA* 3.6 14.3 - - + +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ARG 3.0 22.5 + - - +
104A GLU 3.9 0.2 - - - +
105A ILE 3.1 0.4 - - - -
106A LEU* 1.3 75.5 - - - +
108A GLU* 1.3 59.2 + - - +
110A THR* 3.5 3.0 + - - -
111A GLY 3.3 3.8 + - - -
112A ARG* 3.0 31.8 + - + +
114A GLY 3.8 1.1 - - - +
115A GLY* 3.3 26.4 - - - +
323A PHE* 3.6 19.1 - - + -
324A ALA* 3.4 13.1 - - + +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLU 3.4 10.1 + - - +
105A ILE 2.9 9.4 + - - +
107A ALA* 1.3 73.7 - - - +
109A LEU* 1.3 68.0 + - - +
110A THR 3.1 1.6 - - - -
111A GLY* 3.0 11.0 + - - +
115A GLY* 3.5 1.2 - - - -
116A CYS* 3.5 11.2 + - - +
117A ALA* 2.9 32.2 + - + +
118A LYS 3.4 0.5 + - - -
119A GLY* 2.9 39.2 + - - -
121A GLY 3.2 2.6 + - - -
122A GLY* 2.9 40.7 + - - +
126A MET* 4.3 11.2 - - + -
304D TYR* 3.3 14.7 - - - -
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Residues in contact with LEU 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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45A MET* 6.2 1.1 - - + -
49A ALA* 3.6 30.1 - - + -
58A ILE* 3.1 32.3 - - + +
62A CYS* 4.7 2.7 - - - -
92A HIS* 3.9 26.5 - - + +
105A ILE* 3.1 17.0 + - + +
106A LEU* 3.2 21.1 + - + +
108A GLU* 1.3 78.6 - - - +
110A THR* 1.3 57.9 + - - +
122A GLY 4.6 0.2 - - - -
123A SER* 3.5 39.0 - - - +
126A MET* 4.6 5.6 - - - -
304D TYR* 2.9 25.5 + - - -
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Residues in contact with THR 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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52A LEU* 4.7 13.0 - - + -
57A ILE* 3.4 46.0 - - + +
58A ILE* 3.8 14.1 - - + -
106A LEU 2.9 18.1 + - - +
107A ALA 3.5 6.2 + - - -
108A GLU 3.1 0.4 - - - -
109A LEU* 1.3 76.3 - - - +
111A GLY* 1.3 58.6 + - - +
112A ARG* 3.0 25.7 + - - +
324A ALA* 2.9 29.9 + - + +
329A GLU* 5.4 0.3 - - - +
304D TYR* 4.6 1.6 - - - -
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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