Contacts of the strand formed by residues 434 - 437 (chain J) in PDB entry 6ALG
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 ILE 434 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1270I PHE* 3.6 32.8 - - + -
1274I GLU* 3.7 26.9 - - + +
1277I ALA* 3.8 15.8 - - + +
1278I LEU* 4.6 5.8 - - + -
1281I TYR* 3.0 28.6 + - + -
422J LEU* 4.0 28.5 - - + -
423J LEU 3.4 7.6 - - - +
424J ASN* 3.5 24.5 - - + +
428J THR* 4.5 1.9 - - - +
431J ARG 3.6 2.4 + - - +
433J GLY* 1.3 75.6 - - - +
435J GLN* 1.3 65.4 + - - +
469J HIS* 5.7 0.4 - - + -
484J MET* 4.0 10.9 - - + +
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Residues in contact with GLN 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281I TYR* 4.3 6.1 - - - +
422J LEU* 3.3 7.0 - - - +
423J LEU 2.9 31.5 + - - +
432J LEU* 3.5 43.0 + - - +
434J ILE* 1.3 82.3 - - - +
436J ALA* 1.3 62.6 + - - +
437J PHE* 4.0 6.5 - - + -
453J VAL* 3.3 24.3 - - - +
456J ALA* 4.0 14.6 - - - +
457J TYR* 3.3 15.9 + - - +
484J MET* 3.7 10.1 - - - +
486J SER* 3.3 19.7 + - - -
489J ASN* 4.6 11.2 + - - +
499J ILE* 5.7 0.6 - - - +
500J ILE* 5.8 2.0 - - - +
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Residues in contact with ALA 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420J PRO* 4.6 2.9 - - + -
421J VAL 3.0 13.5 - - - +
422J LEU* 3.8 16.2 - - + -
435J GLN* 1.3 76.5 - - - +
437J PHE* 1.3 63.7 + - - +
480J ALA* 3.8 23.1 - - + +
484J MET* 2.9 20.5 + - + +
485J MET* 3.4 7.6 - - - +
486J SER* 3.2 23.9 + - - -
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Residues in contact with PHE 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363J LEU 4.2 6.1 - - - -
364J HIS 4.4 0.4 - - - -
365J GLN 3.6 20.4 - - - -
366J CYS* 3.6 23.6 - - + +
420J PRO* 3.0 12.0 - - - +
421J VAL* 2.9 29.5 + - + +
423J LEU* 3.7 35.9 - - + -
435J GLN* 4.0 11.0 - - + -
436J ALA* 1.3 75.2 - - - +
438J GLU* 1.3 63.8 + - - +
449J LEU* 3.9 11.4 - - + -
450J HIS* 5.0 2.7 - - + -
453J VAL* 3.7 28.5 - - + -
457J TYR* 3.6 20.4 - - - -
485J MET* 4.1 6.7 - - - -
486J SER* 3.6 28.7 - - - -
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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