Contacts of the strand formed by residues 245 - 250 (chain B) in PDB entry 2AVD
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG* 2.8 29.0 + - - +
195B TYR* 3.6 22.0 - - - +
199B LEU* 3.6 29.4 - - + -
239B ILE* 4.6 0.9 - - + +
242B ASP* 3.3 21.7 - - + +
243B VAL 3.2 4.0 - - - +
244B ARG* 1.3 82.9 - - - +
246B TYR* 1.3 58.1 + - - +
247B ILE* 3.6 20.0 - - + -
259B ALA* 4.1 17.7 - - + -
260B PHE 3.1 16.8 - - - +
261B LYS* 4.2 0.2 - - - -
262B ILE* 4.1 4.9 - - - +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 4.2 6.3 - - - +
96A ASN* 3.3 46.4 - - + +
99A ARG* 3.5 47.5 + - + +
100A LEU* 3.2 26.7 + - - +
205B GLY* 5.4 2.3 - - - -
245B VAL* 1.3 72.4 - - - +
247B ILE* 1.3 62.6 + - - +
260B PHE* 2.8 68.3 + + + +
261B LYS 4.5 5.4 + - - -
262B ILE* 3.6 24.5 - - + -
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG 3.5 25.6 - - - +
62A SER* 3.6 20.9 - - - +
64A ARG* 3.8 26.5 - - - +
92A GLN* 2.8 28.5 + - - +
96A ASN* 2.9 15.4 + - - +
239B ILE* 3.8 28.9 - - + +
240B ARG* 4.2 2.2 - - - -
245B VAL* 3.6 25.6 - - + -
246B TYR* 1.3 81.8 - - - +
248B SER* 1.3 59.8 + - - +
257B THR* 4.9 3.6 - - + -
258B LEU 3.3 5.8 - - - +
259B ALA* 3.9 10.5 - - + -
260B PHE* 4.8 0.2 - - - -
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A SER* 4.5 3.4 - - - -
89A GLU 4.9 1.2 + - - -
92A GLN* 4.3 2.8 - - - +
93A LEU* 3.5 38.8 + - - +
96A ASN* 3.0 22.9 + - - +
247B ILE* 1.3 72.4 + - - +
249B LEU* 1.3 60.3 + - - +
250B LEU* 4.1 12.3 - - - +
256B LEU 3.7 1.2 - - - +
257B THR* 3.5 3.3 - - - +
258B LEU* 2.8 40.6 + - - +
260B PHE* 4.7 2.0 - - - -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 5.0 0.9 - - + -
58A LEU* 3.5 47.0 - - + +
61A ARG* 4.2 29.2 - - + +
62A SER* 3.7 21.7 + - - +
89A GLU* 5.3 5.7 - - - +
213B VAL* 3.8 22.2 - - + -
214B LEU* 4.2 16.8 - - + -
236B ASN* 4.9 9.9 - - + +
248B SER* 1.3 73.8 - - - +
250B LEU* 1.3 73.4 + - - +
251B PRO* 4.4 0.7 - - - +
256B LEU 3.4 3.4 - - - +
257B THR* 3.5 22.7 - - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.1 3.4 - - - -
89A GLU* 5.8 2.2 - - + +
93A LEU* 4.3 14.1 - - + -
250A LEU* 4.4 12.6 - - + -
252A LEU* 4.1 26.7 - - + -
93B LEU* 3.7 30.1 - - + -
248B SER* 4.3 15.7 - - - +
249B LEU* 1.3 84.3 - - - +
251B PRO* 1.4 64.8 - - + +
252B LEU* 3.0 19.2 + - + +
255B GLY* 3.6 4.5 - - - -
256B LEU* 2.7 43.5 + - + +
258B LEU* 4.0 16.8 - - + -
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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