Contacts of the strand formed by residues 115 - 119 (chain D) in PDB entry 1TW8
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 115 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLU* 3.9 14.4 - - - +
41D VAL* 4.7 4.5 - - + -
42D TYR* 3.9 24.7 - - + -
45D LEU* 4.6 4.3 - - + -
53D THR* 3.6 25.1 - - + -
54D PHE 3.3 13.0 - - - +
55D LYS* 4.7 0.4 - - - +
56D GLN 5.2 0.2 - - - -
113D ALA* 3.9 4.9 - - - +
114D ASP* 1.3 99.3 - - + +
116D LEU* 1.3 62.9 + - - +
117D LEU* 3.6 22.2 + - + -
126D LEU* 3.0 38.3 + - + +
128D VAL* 3.8 22.2 - - + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU 3.6 4.9 - - - +
54D PHE* 2.7 29.0 + - - +
55D LYS 4.6 6.2 - - - +
56D GLN* 3.6 13.2 - - - +
59D TYR* 3.7 28.9 - - + -
89D LEU* 3.4 35.9 - - + -
113D ALA* 4.9 0.9 - - + -
115D ILE* 1.3 72.9 - - - +
117D LEU* 1.3 56.4 + - - +
118D VAL* 3.1 11.8 + - + +
123D TYR* 4.4 15.7 - - + -
124D GLU 4.1 2.9 - - - +
125D LEU* 3.3 43.3 - - + -
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PHE* 3.7 15.4 - - + -
4D ILE* 3.3 34.8 - - + -
45D LEU* 4.2 6.7 - - + -
49D LEU* 4.1 15.5 - - + -
52D LEU* 3.1 9.2 - - + +
53D THR* 3.4 26.2 - - - +
115D ILE* 3.6 22.7 - - + -
116D LEU* 1.3 68.7 - - - +
118D VAL* 1.3 58.8 + - - +
124D GLU* 3.0 48.2 + - - +
126D LEU* 3.6 24.7 - - + -
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PHE* 4.1 0.7 - - - -
51D ASP 4.1 3.8 - - - +
52D LEU* 3.0 22.9 + - - +
54D PHE* 4.2 11.7 - - + -
59D TYR* 3.9 30.3 - - + +
116D LEU* 3.8 10.5 - - + +
117D LEU* 1.3 75.2 - - - +
119D LYS* 1.3 65.5 + - - +
120D ASP* 4.1 7.2 - - - +
121D GLN 4.9 1.8 - - - +
122D PHE 3.2 15.9 - - - +
123D TYR* 3.4 40.8 - - + +
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PHE* 3.6 18.8 - - + -
51D ASP 5.6 0.4 - - - -
52D LEU* 3.3 35.7 - - + -
118D VAL* 1.3 78.0 - - - +
120D ASP* 1.3 75.2 + - - +
122D PHE* 3.1 9.6 + - - +
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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