Contacts of the strand formed by residues 337 - 340 (chain X) in PDB entry 2GLJ
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 GLU 337 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99X PHE 3.0 9.4 + - - +
100X LYS* 3.0 38.9 + - + +
101X ILE 3.0 22.3 + - - +
285X LYS* 5.7 2.4 + - - +
335X ASN 4.9 4.3 - - - +
336X SER* 1.3 78.6 - - - +
338X MET* 1.3 60.5 + - - +
388X TYR* 3.6 36.9 - - + +
391X GLU* 5.6 5.2 - - - +
428X MET* 4.1 2.0 - - - -
429X GLN* 3.7 11.3 - - + +
462X PHE* 3.9 9.4 - - + -
465X ASN* 4.5 5.2 - - - +
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Residues in contact with MET 338 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ILE* 3.4 22.7 - - + +
103X GLY* 4.6 6.3 - - - +
290X ILE* 5.0 0.9 - - - -
337X GLU* 1.3 73.9 - - - +
339X LEU* 1.3 74.6 + - - +
340X SER* 3.5 23.1 - - - +
388X TYR* 2.9 17.3 + - - -
419X ILE 4.9 1.3 - - - +
420X ALA* 4.0 6.3 - - - +
423X LEU* 3.2 50.7 - - + -
428X MET* 3.0 22.5 - - + +
429X GLN 3.0 13.0 + - - +
430X VAL* 3.6 38.3 - - + -
431X ILE 3.9 1.2 + - - -
462X PHE* 4.5 0.7 - - - -
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Residues in contact with LEU 339 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ILE 3.1 4.4 + - - +
102X LEU* 3.6 16.8 - - + +
103X GLY 3.8 9.8 + - - +
338X MET* 1.3 86.9 - - - +
340X SER* 1.3 59.8 + - - +
341X SER* 2.9 16.9 + - - -
367X ILE* 5.8 1.1 - - + -
369X PHE* 5.1 2.9 - - + -
388X TYR* 3.6 11.0 - - - +
392X LEU* 4.0 12.6 - - + -
396X LEU* 6.5 0.2 - - + -
431X ILE* 3.6 25.1 - - + -
433X CYS* 3.6 20.6 - - + -
458X GLY 4.9 3.4 - - - +
459X TYR* 4.0 27.1 - - + -
462X PHE* 3.9 31.4 - - + -
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Residues in contact with SER 340 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X GLY* 3.8 11.8 + - - +
338X MET* 3.5 30.0 - - - +
339X LEU* 1.3 70.5 - - - +
341X SER* 1.3 60.9 + - - +
342X ASP* 6.0 0.2 - - - +
418X THR* 5.2 0.7 - - - -
419X ILE* 3.9 17.0 + - - +
420X ALA* 3.7 28.7 + - - +
430X VAL* 3.9 5.3 - - - +
431X ILE 3.3 16.5 + - - +
432X ASP* 3.4 10.9 + - - +
433X CYS 3.3 7.3 + - - -
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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