Contacts of the strand formed by residues 240 - 244 (chain A) in PDB entry 5V8V
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 GLY 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE 3.8 0.2 - - - -
78A LEU* 2.8 38.1 + - - -
86A TYR* 4.8 1.1 - - - -
227A TYR* 3.2 20.4 - - - -
228A TYR* 4.5 1.3 - - - -
238A LEU* 3.4 14.9 - - - +
239A GLY* 1.3 77.9 - - - +
241A GLN* 1.3 65.4 + - - +
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Residues in contact with GLN 241 (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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75A SER* 3.2 24.2 + - - -
76A VAL 3.4 11.7 - - - +
77A ILE* 4.1 12.5 - - + +
78A LEU* 3.8 6.0 - - - +
225A SER 4.1 0.5 - - - +
226A PHE* 3.6 1.0 - - - -
227A TYR* 2.8 43.7 + - + +
238A LEU* 4.2 12.6 - - + +
240A GLY* 1.3 75.9 - - - +
242A ILE* 1.3 74.0 + - - +
243A VAL* 3.9 6.8 - - + +
248A ASP* 3.1 40.5 + - - +
251A HIS* 3.8 11.5 + - - -
390A TYR* 5.1 1.1 + - - -
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Residues in contact with ILE 242 (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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75A SER* 3.3 5.4 - - - -
76A VAL* 2.9 56.4 + - + +
78A LEU* 4.0 14.3 - - + +
103A PHE* 4.3 19.7 - - + -
196A MET* 4.1 21.1 - - + -
224A PHE* 4.5 1.3 - - + -
225A SER 3.1 15.3 - - - +
226A PHE* 3.7 37.0 - - + +
241A GLN* 1.3 72.8 - - - +
243A VAL* 1.3 73.1 + - - +
244A LEU* 4.2 11.8 - - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 4.5 11.9 - - - +
74A SER 3.5 13.0 - - - +
75A SER* 4.4 4.5 - - - -
224A PHE* 3.1 8.3 - - - +
225A SER* 2.9 30.7 + - - +
241A GLN* 3.9 22.9 - - + +
242A ILE* 1.3 79.2 - - - +
244A LEU* 1.3 65.6 + - - +
246A GLY* 3.4 33.1 - - - +
247A SER 4.3 3.1 - - - +
248A ASP* 4.2 8.7 - - + +
390A TYR* 3.7 20.2 - - - +
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 3.2 4.2 - - - -
74A SER* 2.7 45.9 + - - +
76A VAL* 5.1 5.6 - - + -
103A PHE* 6.3 0.9 - - + -
165A VAL* 4.0 44.2 - - + +
168A ILE* 4.3 4.3 - - + -
196A MET* 4.2 15.0 - - + -
210A PHE* 4.1 15.3 - - + -
213A ILE* 4.3 12.8 - - + -
219A LEU* 3.8 18.1 - - + +
223A VAL 4.2 1.6 - - - -
224A PHE* 4.0 18.4 - - + -
242A ILE* 4.2 13.0 - - + +
243A VAL* 1.3 71.2 - - - +
245A GLY* 1.3 59.4 + - - +
246A GLY 3.5 0.4 - - - -
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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