Contacts of the strand formed by residues 113 - 118 (chain H) in PDB entry 3DUF
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 THR 113 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76H PRO 3.3 6.7 + - - -
77H VAL* 3.3 9.7 - - - +
78H PRO* 3.2 20.1 - - - +
111H PRO 5.5 0.2 - - - -
112H ILE* 1.3 76.6 + - - +
114H ILE* 1.3 64.9 + - - +
115H ARG* 4.8 3.8 - - + -
157H LEU* 4.4 9.0 - - + -
160H ALA* 2.9 44.0 + - + +
161H ILE* 3.3 31.6 + - + +
167H VAL* 3.4 10.3 - - - +
169H PHE* 4.4 11.7 - - + -
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Residues in contact with ILE 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H GLY* 6.1 2.0 - - - -
78H PRO* 3.3 28.0 - - + +
80H ILE* 3.7 35.7 - - + -
83H PHE* 6.0 2.7 - - + -
93H ILE* 4.8 16.4 - - + -
97H MET* 4.4 22.7 - - + -
112H ILE* 3.8 15.7 - - + +
113H THR* 1.3 70.9 - - - +
115H ARG* 1.3 62.0 + - - +
116H SER* 5.2 2.0 - - - -
142H LEU* 6.5 0.4 - - + -
166H PRO* 6.2 0.4 - - + -
167H VAL 2.8 16.5 + - - +
168H ILE* 3.7 19.3 - - + +
169H PHE* 2.8 33.7 + - - +
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Residues in contact with ARG 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 3.9 10.2 - - - +
13H LEU* 4.2 27.5 - - - +
25H ILE* 5.2 5.3 - - - +
39H ALA* 3.4 27.1 - - - +
40H THR* 4.3 13.3 - - - +
77H VAL* 4.2 16.9 + - + +
78H PRO 3.1 12.2 + - - +
79H GLU* 2.9 37.1 + - - +
80H ILE* 3.0 25.5 + - - +
113H THR* 3.9 2.0 + - + -
114H ILE* 1.3 75.0 - - - +
116H SER* 1.3 63.0 + - - +
117H PRO* 5.9 0.2 - - - +
157H LEU* 4.5 11.2 - - + -
169H PHE* 3.5 17.3 - - + +
171H GLU* 3.0 37.3 + - - +
176H TYR* 4.8 0.6 + - - -
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Residues in contact with SER 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ILE* 3.0 29.0 + - - +
82H PHE 3.4 0.5 - - - -
83H PHE* 3.0 41.0 + - - -
114H ILE* 4.2 2.0 + - - -
115H ARG* 1.3 77.8 - - - +
117H PRO* 1.3 68.7 - - - +
118H PHE 4.0 0.2 + - - -
168H ILE* 6.2 0.7 - - - -
169H PHE 3.1 7.5 + - - -
170H LEU* 3.4 14.6 - - - +
171H GLU* 3.1 23.3 + - - -
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Residues in contact with PRO 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H PHE* 4.4 9.0 - - + -
79H GLU* 5.3 6.5 - - + -
80H ILE 3.6 4.3 - - - +
81H GLN 2.9 29.6 - - - +
82H PHE* 3.7 8.4 - - + -
83H PHE* 3.1 24.6 + - - +
115H ARG* 4.8 1.1 - - - +
116H SER* 1.3 83.4 - - - +
118H PHE* 1.3 61.4 + - - +
171H GLU* 2.9 14.6 - - - +
173H LEU* 3.6 23.6 - - + -
176H TYR* 3.2 25.6 - - - +
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Residues in contact with PHE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H PHE* 4.0 16.6 - + + -
117H PRO* 1.3 77.2 - - - +
119H GLY* 1.3 74.8 + - - +
128H HIS 4.2 10.3 - - - -
130H ASP 3.8 15.0 - - - +
131H SER* 3.9 23.8 - - - -
132H LEU 5.3 0.4 - - - -
133H GLU* 4.1 13.9 - - - -
146H ILE* 4.1 21.5 - - + -
170H LEU* 3.7 32.3 - - + -
171H GLU 3.0 7.9 + - - -
172H HIS* 3.4 44.4 - + + -
173H LEU* 2.9 27.8 + - - +
209H TYR* 5.7 4.5 - + - -
210H GLY* 5.3 2.7 - - - -
261H GLU* 5.1 2.9 - - + -
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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