Contacts of the strand formed by residues 397 - 402 (chain B) in PDB entry 2G9Y
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 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 3.4 14.6 - - - -
283B ALA* 4.1 9.6 - - + -
379B PRO* 4.4 22.0 - - + +
389B ALA* 3.7 27.4 - - + -
390B LEU 3.2 4.9 - - - +
391B ASN* 4.0 19.1 - - - +
396B ALA* 1.3 77.7 - - - +
398B MET* 1.3 66.2 + - - +
399B VAL* 4.3 8.3 - - + -
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Residues in contact with MET 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 3.6 16.4 - - + -
60B ALA* 3.5 25.6 - - - +
63B ASN* 3.6 33.2 - - + -
64B TYR* 4.1 13.9 - - + +
339B ILE* 4.4 0.2 - - + -
376B ILE* 4.0 19.1 - - + -
379B PRO* 5.9 0.2 - - - -
388B GLN 3.7 0.9 - - - +
389B ALA* 3.5 0.3 - - - -
390B LEU* 2.7 52.1 + - + +
392B THR* 3.7 12.3 - - + -
396B ALA 3.9 0.4 + - - -
397B VAL* 1.3 74.8 - - - +
399B VAL* 1.3 72.7 + - - +
400B MET* 3.9 24.6 + - - -
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 6.0 0.2 - - - +
278B ASN* 3.7 32.1 - - + +
376B ILE* 3.5 8.3 - - - +
377B VAL* 2.9 54.5 + - + +
378B ALA 3.9 1.3 - - - +
379B PRO* 3.5 33.3 - - + +
381B THR* 5.1 0.2 - - - -
387B THR* 4.4 3.1 - - + -
388B GLN 3.3 9.2 - - - +
389B ALA* 4.2 9.6 - - + -
397B VAL* 4.3 5.1 + - + -
398B MET* 1.3 78.9 - - - +
400B MET* 1.3 71.5 + - - +
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Residues in contact with MET 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA* 3.7 17.3 - - + -
335B PRO* 3.9 22.0 - - + -
338B GLN* 3.4 30.3 - - - +
339B ILE* 4.1 5.8 - - + -
374B SER* 3.9 10.8 - - - -
375B GLN 3.1 7.2 - - - +
376B ILE* 4.6 3.6 - - + -
377B VAL* 4.7 0.2 - - - -
387B THR* 3.3 8.5 - - - +
388B GLN* 3.1 29.7 + - - +
390B LEU* 3.6 24.2 - - + -
398B MET* 3.9 23.6 - - + -
399B VAL* 1.3 80.1 - - - +
401B SER* 1.3 62.4 + - - +
402B TYR* 3.6 19.8 - - + +
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLY 4.2 10.6 + - - -
404A ASN* 4.4 4.5 - - - +
373B ALA 3.8 1.9 - - - +
374B SER* 3.4 4.9 - - - -
375B GLN* 2.7 42.6 + - - +
377B VAL* 4.1 21.3 - - - -
383B ALA* 4.2 8.0 - - - +
385B GLY* 5.6 0.3 - - - -
386B LEU 3.4 5.5 + - - -
387B THR* 3.8 16.7 - - - +
400B MET* 1.3 76.8 - - - +
402B TYR* 1.3 71.1 + - - +
403B GLY 4.0 3.0 + - - -
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Residues in contact with TYR 402 (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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273B ALA* 4.1 6.1 - - + -
330B ASP* 3.2 42.6 - - - -
333B ALA* 3.8 26.7 - - + -
334B ASN 4.0 0.7 + - - -
335B PRO* 3.5 40.8 - - + +
338B GLN* 2.8 17.6 + - - -
373B ALA* 4.1 6.1 - - + -
374B SER* 3.4 19.1 - - - -
385B GLY* 3.6 1.2 - - - -
386B LEU* 2.8 42.0 + - + +
400B MET* 3.6 12.8 - - + +
401B SER* 1.3 79.4 + - - +
403B GLY* 1.3 58.4 + - - +
405B SER 5.4 0.7 - - - +
410B GLN* 3.2 29.8 + - + +
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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
------------------------------------------------------------
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