Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 6D3N
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLN* 3.5 34.3 - - + +
95A LEU 3.3 13.0 - - - +
96A VAL* 4.4 8.5 - - + -
109A TRP* 4.0 3.5 - - - -
112A ASP* 5.6 1.3 - - - +
144A PHE* 4.7 6.2 - - + -
145A PHE* 3.1 7.8 - - - +
146A GLN* 3.1 51.1 + - + +
231A GLY 4.1 16.6 - - - +
232A ALA 3.9 6.0 + - - +
233A THR* 1.3 81.2 - - - +
235A LEU* 1.3 65.2 + - - +
236A GLY 4.5 0.7 - - - +
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Residues in contact with LEU 235 (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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93A ALA 4.7 0.2 - - - -
94A GLN* 3.4 1.7 - - - -
95A LEU* 2.8 43.7 + - + +
109A TRP* 3.6 22.7 - - + -
133A LEU* 4.4 24.5 - - + -
143A VAL* 3.9 22.0 - - + -
144A PHE 3.5 15.5 - - - +
145A PHE* 4.1 16.6 - - + -
165A LEU* 4.4 13.9 - - + -
179A LEU* 5.4 0.2 - - + -
212A LEU* 5.0 4.9 - - + -
214A VAL* 3.8 22.7 - - + -
234A VAL* 1.3 75.7 - - - +
236A GLY* 1.3 60.5 + - - +
237A LEU* 5.6 1.9 - - + +
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Residues in contact with GLY 236 (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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93A ALA 3.3 9.6 - - - -
94A GLN* 4.0 4.5 - - - -
143A VAL* 3.5 2.8 - - - +
144A PHE* 2.9 59.7 + - - +
235A LEU* 1.3 76.9 - - - +
237A LEU* 1.3 65.1 + - - +
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Residues in contact with LEU 237 (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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92A PHE* 3.2 4.1 - - - +
93A ALA* 2.8 64.3 + - + +
124A LEU* 4.8 5.8 - - + -
133A LEU* 4.2 16.6 - - + -
135A VAL* 4.9 5.2 - - + -
141A TYR* 3.9 25.4 - - + -
142A TYR 3.1 15.0 - - - +
143A VAL* 3.9 13.7 - - + -
144A PHE* 3.8 4.4 - - - -
206A LEU* 4.0 20.9 - - + -
212A LEU* 4.6 12.3 - - + -
235A LEU* 5.6 3.4 - - + +
236A GLY* 1.3 77.8 - - - +
238A PHE* 1.3 66.8 + - - +
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Residues in contact with PHE 238 (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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91A MET 3.5 7.4 - - - +
92A PHE* 3.7 15.7 - - + +
141A TYR* 3.3 7.5 - - - -
142A TYR* 2.9 69.6 + + + -
144A PHE* 4.0 15.3 - + - -
237A LEU* 1.3 80.3 - - - +
239A ARG* 1.3 72.0 + - - +
240A VAL* 4.5 7.6 - - + -
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Residues in contact with ARG 239 (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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91A MET* 3.0 31.6 + - + +
137A LYS* 4.5 9.6 - - - +
138A ALA 2.6 34.2 + - - -
139A GLY* 3.8 1.6 - - - -
140A VAL 3.6 12.1 - - - +
141A TYR* 3.5 33.1 - - + -
238A PHE* 1.3 79.5 - - - +
240A VAL* 1.3 63.4 + - - +
241A THR* 3.4 49.8 - - - +
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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