Contacts of the strand formed by residues 397 - 402 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ALA* 4.3 10.1 - - + -
379A PRO* 4.2 23.7 - - + +
389A ALA* 4.0 24.2 - - + -
390A LEU 3.3 2.9 - - - +
391A ASN* 4.1 19.3 - - - +
396A ALA* 1.3 76.0 - - - +
398A MET* 1.3 67.1 + - - +
399A VAL* 4.2 8.5 - - + -
98B TYR* 3.6 12.6 - - - -
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Residues in contact with MET 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 3.4 26.0 - - - +
63A ASN* 3.4 35.2 - - + -
64A TYR* 4.2 16.8 - - + +
339A ILE* 4.4 1.6 - - + -
376A ILE* 4.1 19.7 - - + -
379A PRO* 5.8 0.2 - - - -
388A GLN 3.7 1.0 - - - +
389A ALA* 3.5 0.3 - - - -
390A LEU* 2.8 42.1 + - + +
392A THR* 3.7 11.2 - - + -
396A ALA 3.9 0.2 + - - -
397A VAL* 1.3 75.0 - - - +
399A VAL* 1.3 68.5 + - - +
400A MET* 3.9 25.8 - - + -
98B TYR* 3.5 18.6 - - + -
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 3.6 31.0 - - + +
376A ILE* 3.5 6.8 - - - +
377A VAL* 2.9 55.9 + - + +
378A ALA 3.9 1.1 - - - +
379A PRO* 3.4 34.5 - - + +
387A THR* 4.3 3.8 - - - -
388A GLN 3.3 8.7 - - - +
389A ALA* 4.3 4.3 - - + -
397A VAL* 4.2 11.4 - - + -
398A MET* 1.3 79.7 - - - +
400A MET* 1.3 72.0 + - - +
98B TYR* 6.0 0.2 - - - +
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Residues in contact with MET 400 (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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60A ALA* 3.7 17.9 - - + -
335A PRO* 3.8 19.3 - - + -
338A GLN* 3.5 28.7 - - - +
339A ILE* 3.8 21.1 - - + -
374A SER* 3.9 10.3 - - - -
375A GLN 3.2 7.6 - - - +
376A ILE* 4.9 2.9 - - + -
387A THR* 3.2 8.1 - - - -
388A GLN 3.0 30.9 + - - +
390A LEU* 3.7 23.6 - - + -
398A MET* 3.9 15.9 - - + -
399A VAL* 1.3 78.9 - - - +
401A SER* 1.3 60.7 + - - +
402A TYR* 3.7 20.4 - - + +
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Residues in contact with SER 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA 3.8 1.9 - - - +
374A SER* 3.4 5.0 - - - -
375A GLN* 2.7 44.2 + - - +
377A VAL* 3.9 22.4 - - - -
383A ALA* 4.2 6.8 - - - +
385A GLY* 5.6 0.2 - - - -
386A LEU 3.5 4.3 + - - -
387A THR* 3.9 15.4 - - - +
400A MET* 1.3 74.7 - - - +
402A TYR* 1.3 65.6 + - - +
403A GLY* 4.0 7.5 + - - -
403B GLY 4.2 11.8 + - - -
404B ASN* 4.3 5.3 - - - +
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Residues in contact with TYR 402 (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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273A ALA* 4.1 6.1 - - + -
330A ASP* 3.3 42.6 - - - -
333A ALA* 3.7 29.2 - - + -
334A ASN 3.9 0.7 - - - -
335A PRO* 3.5 39.6 - - + +
338A GLN* 2.9 17.9 + - - -
373A ALA* 4.4 4.7 - - + -
374A SER* 3.6 17.9 - - - -
385A GLY* 3.6 1.2 - - - -
386A LEU* 2.8 40.1 + - + +
400A MET* 3.7 15.6 - - + +
401A SER* 1.3 78.0 + - - +
403A GLY* 1.3 58.9 + - - +
410A GLN* 3.2 34.5 + - + +
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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