Contacts of the strand formed by residues 307 - 312 (chain C) in PDB entry 1Q57
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 307 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C GLU* 1.3 74.2 - - - +
308C ILE* 1.3 65.0 + - - +
309C MET* 4.9 3.6 - - + -
446C MET* 4.5 11.9 - - + -
449C LEU* 5.4 1.6 - - + -
450C LYS* 3.6 25.6 - - + +
453C ALA* 3.4 31.0 - - + -
460C LEU* 3.3 23.1 - - + +
462C VAL* 5.3 4.7 - - + -
495C LEU 4.5 0.9 - - - +
496C SER* 3.6 29.2 - - - +
497C ASP* 2.8 32.1 + - - +
498C THR 3.6 3.8 + - - -
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PHE* 3.6 33.0 - - + -
301C GLY 4.2 1.6 - - - +
302C ALA* 3.9 20.0 - - + -
306C GLU* 3.7 25.8 - - + +
307C VAL* 1.3 73.3 - - - +
309C MET* 1.3 58.8 + - - +
310C VAL* 4.1 1.6 - - + -
459C VAL* 4.7 10.1 - - + -
460C LEU 2.9 8.4 + - - +
461C VAL* 3.2 18.6 - - + -
462C VAL* 2.8 33.0 + - - +
498C THR* 3.5 26.5 - - - +
500C ILE* 3.9 15.3 - - + -
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Residues in contact with MET 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL* 4.9 2.0 - - + -
308C ILE* 1.3 73.2 - - - +
310C VAL* 1.3 66.2 + - - +
311C THR* 4.0 5.5 + - - -
426C ILE* 5.6 0.2 - - + -
446C MET* 3.5 24.2 - - + -
462C VAL* 3.2 42.4 - - + +
464C CYS* 4.4 11.9 - - + -
486C LEU* 5.6 5.4 - - + -
492C LEU* 3.7 27.4 - - + -
496C SER* 3.6 15.0 - - - +
498C THR 2.9 7.9 + - - -
499C ILE* 3.2 27.2 - - + +
500C ILE 3.0 26.2 + - - +
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Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PHE* 6.2 0.2 - - + -
308C ILE* 4.8 5.6 - - + -
309C MET* 1.3 71.1 - - - +
311C THR* 1.3 64.7 + - - +
318C MET* 3.7 12.3 - - + +
321C PHE* 4.2 24.7 - - + -
322C VAL* 3.8 18.4 - - + -
461C VAL* 3.9 20.9 - - + -
462C VAL 3.0 5.1 + - - +
463C ILE* 3.4 10.8 - - + -
464C CYS* 2.8 27.7 + - - +
500C ILE* 3.3 10.5 - - + +
502C LEU* 3.5 24.7 - - + -
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Residues in contact with THR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C MET* 4.9 7.0 - - - -
310C VAL* 1.3 78.1 - - - +
312C SER* 1.3 74.3 + - - +
318C MET* 3.7 4.7 - - - -
464C CYS* 2.6 27.9 + - - -
466C LEU* 3.0 23.4 - - + +
481C VAL* 4.6 8.7 - - + -
486C LEU* 4.7 10.0 - - + +
499C ILE* 5.1 7.6 - - + -
500C ILE 3.0 8.4 + - - +
501C ALA* 3.1 20.5 - - + -
502C LEU* 3.0 18.3 + - - +
519C LEU* 5.1 0.2 - - + -
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C THR* 1.3 83.9 + - - +
313C GLY* 1.3 73.8 + - - +
315C GLY* 3.8 12.5 + - - -
317C VAL* 5.3 1.2 - - - +
318C MET* 3.0 21.7 + - - +
465C HIS* 4.3 0.5 - - - +
466C LEU* 3.5 30.0 + - - +
481C VAL* 5.3 2.7 - - - -
501C ALA* 5.3 0.2 - - - -
502C LEU* 2.4 40.8 + - - +
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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