Contacts of the strand formed by residues 113 - 119 (chain A) in PDB entry 1DMN
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 ILE 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TYR* 4.0 12.6 - - + -
31A MET* 2.8 32.2 + - + +
32A PHE* 3.5 37.6 - - + -
33A ALA* 2.9 24.8 + - - -
36A ALA* 3.3 9.4 - - - +
105A MET* 3.8 31.6 - - + -
106A ARG 3.7 4.9 - - - +
107A PHE* 3.8 22.2 - - + -
112A ARG* 1.3 69.2 - - - +
114A GLN* 1.3 60.0 + - - +
115A THR 3.5 23.8 - - - +
116A MET* 4.2 4.3 - - + -
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Residues in contact with GLN 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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33A ALA* 4.4 8.1 - - + -
35A ASP* 6.0 0.9 - - - +
36A ALA* 3.3 9.9 - - - -
37A THR* 3.3 22.5 + - - +
106A ARG* 2.8 37.4 + - - +
107A PHE 4.4 1.4 - - - +
108A ASP* 3.4 35.3 - - + +
109A GLU* 4.4 10.1 + - - -
112A ARG 3.3 1.0 + - - -
113A ILE* 1.3 74.3 - - - +
115A THR* 1.3 67.0 + - - +
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Residues in contact with THR 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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37A THR* 3.6 18.2 + - - +
39A GLU* 4.9 6.1 + - - -
105A MET* 3.4 4.3 - - - -
106A ARG* 3.1 56.0 + - + +
113A ILE* 3.5 6.7 - - - +
114A GLN* 1.3 84.0 - - + +
116A MET* 1.3 65.2 + - - +
117A GLN* 4.7 14.1 + - - +
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Residues in contact with MET 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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16A TYR* 3.1 31.6 - - + +
32A PHE* 4.2 19.7 - - + -
37A THR 3.2 9.1 + - - +
38A VAL* 3.5 22.3 - - + -
39A GLU* 2.9 26.2 + - - +
40A ASP* 4.3 13.0 - - - +
56A PHE* 5.6 0.2 - - + -
57A PHE* 4.6 5.2 - - + -
103A ASP* 3.7 24.7 - - - +
104A VAL 3.5 4.0 - - - +
105A MET* 3.7 24.5 - - + -
113A ILE* 4.2 9.4 - - + -
115A THR* 1.3 77.6 + - - +
117A GLN* 1.3 72.7 + - - +
118A ALA 4.6 0.4 - - - -
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Residues in contact with GLN 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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39A GLU* 3.3 27.6 + - + +
42A PHE* 3.6 30.8 - - + -
102A ILE 3.8 1.0 - - - +
103A ASP* 3.4 4.2 - - - +
104A VAL* 2.9 50.1 + - + +
115A THR* 4.7 14.4 - - - +
116A MET* 1.3 83.8 - - - +
118A ALA* 1.3 60.6 + - - +
119A TYR* 3.9 23.2 + - + -
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Residues in contact with ALA 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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39A GLU 2.9 8.1 + - - -
40A ASP* 3.3 35.9 - - - +
41A PRO* 3.6 3.3 - - - +
42A PHE* 2.8 30.9 + - - +
101A VAL* 4.0 3.8 - - + -
102A ILE 3.5 3.8 - - - -
103A ASP* 3.2 18.2 - - - +
116A MET* 4.7 0.7 - - - -
117A GLN* 1.3 73.4 - - - +
119A TYR* 1.3 62.6 + - - +
120A TRP* 4.0 9.6 - - + -
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Residues in contact with TYR 119 (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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42A PHE* 3.9 38.8 - + + -
100A ASP 4.3 0.3 - - - +
101A VAL* 3.6 1.6 - - - -
102A ILE* 2.8 49.8 + - + +
104A VAL* 3.9 26.4 - - + +
117A GLN* 3.9 31.6 + - + -
118A ALA* 1.3 74.2 - - - +
120A TRP* 1.3 65.8 + - - +
124A ASN* 5.5 0.3 - - - -
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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