Contacts of the strand formed by residues 305 - 310 (chain B) in PDB entry 1QAS
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 TYR 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ASP 2.6 30.1 + - - -
298B MET* 3.3 18.6 - - - -
300B GLN* 3.0 52.0 + - + +
301B PRO 3.1 13.9 - - - -
302B LEU 3.3 13.3 + - - +
303B SER 3.3 1.1 - - - +
304B HIS* 1.3 79.9 - - + +
306B LEU* 1.3 58.5 + - - +
307B VAL* 3.9 1.0 + - - +
428B PRO* 3.7 19.5 - - + -
573B GLN* 2.8 30.1 - - - +
601B TYR* 3.9 31.0 - - + -
602B VAL 3.3 7.2 - - - +
603B LEU* 3.6 29.4 - - + -
604B LYS* 4.2 2.8 - - - +
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Residues in contact with LEU 306 (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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305B TYR* 1.3 71.4 - - - +
307B VAL* 1.3 60.8 + - - +
568B TRP* 3.5 42.4 - - + +
571B GLY 4.4 0.2 - - - +
572B CYS 3.3 26.5 - - - +
573B GLN* 3.8 4.5 - - - +
592B CYS* 4.3 13.5 - - - -
593B PHE* 3.0 30.2 - - + -
600B GLY 3.4 1.9 - - - +
601B TYR* 3.5 1.4 - - - -
602B VAL* 2.9 31.3 + - + +
604B LYS* 3.8 33.2 - - + -
605B PRO* 6.0 2.2 - - + -
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 4.6 7.4 - - + +
305B TYR 4.1 9.4 - - - +
306B LEU* 1.3 75.5 - - - +
308B SER* 1.3 68.5 + - - +
309B SER* 2.9 13.3 + - - +
338B ARG* 3.7 17.5 - - + -
339B CYS* 3.3 31.2 - - - -
386B ILE* 5.2 2.5 - - + -
547B LEU* 4.8 4.9 - - + -
568B TRP* 5.8 0.2 + - - -
573B GLN* 2.7 24.2 + - + +
574B ILE* 4.4 11.4 - - + -
589B TYR* 3.4 6.8 + - - -
593B PHE* 3.6 3.6 - - - -
600B GLY 3.3 3.1 - - - +
601B TYR* 3.5 32.8 - - + +
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Residues in contact with SER 308 (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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307B VAL* 1.3 68.5 - - - +
309B SER* 1.3 58.8 + - - +
335B LYS 4.7 2.1 + - - -
336B GLY 3.8 20.1 + - - -
337B CYS* 3.4 14.9 + - - -
338B ARG* 2.7 28.0 + - - -
339B CYS 3.0 7.8 + - - -
579B PHE* 3.6 15.2 - - - -
589B TYR* 3.8 10.4 - - - -
590B LEU* 4.9 1.4 - - - +
593B PHE* 3.5 26.5 - - - +
600B GLY* 3.0 15.6 + - - -
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Residues in contact with SER 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL 2.9 12.3 + - - -
308B SER* 1.3 72.3 + - - +
310B SER* 1.3 58.5 - - - +
337B CYS* 3.8 3.4 - - - -
339B CYS* 3.2 17.5 - - - +
574B ILE* 2.8 36.4 - - - +
575B VAL 3.2 19.8 - - - +
576B ALA* 3.9 3.4 - - - -
577B LEU 3.1 19.9 + - - -
579B PHE* 3.3 10.5 - - - -
589B TYR* 2.9 10.7 + - - -
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Residues in contact with SER 310 (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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309B SER* 1.3 72.3 - - - +
311B HIS* 1.3 62.0 + - - +
313B THR* 2.7 43.6 + - - +
332B ALA* 4.4 0.8 - - - +
337B CYS* 3.3 20.6 - - - -
339B CYS* 2.8 17.6 + - - +
340B LEU* 4.3 0.2 - - - -
341B GLU* 3.1 18.5 - - - +
576B ALA* 3.9 3.5 - - - +
577B LEU 3.6 6.6 + - - -
579B PHE* 4.0 16.2 + - - +
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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