Contacts of the strand formed by residues 436 - 440 (chain A) in PDB entry 3DLX
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 LYS 436 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 2.7 33.2 + - - -
317A MET* 6.3 3.1 - - + -
395A ASP 2.9 18.0 + - - +
396A LEU* 3.4 14.9 - - + +
397A THR 2.8 27.5 + - - +
435A THR* 1.3 72.7 - - - +
437A VAL* 1.3 62.3 + - - +
438A VAL* 3.7 12.1 - - + -
467A ASN* 3.6 17.7 - - + -
468A ARG* 4.2 24.1 - - - +
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A THR* 3.5 11.0 - - + +
399A LEU* 4.6 9.2 - - + -
410A LEU* 5.3 0.4 - - + -
429A LEU 4.1 20.2 - - - +
430A VAL* 4.1 28.0 - - + +
432A SER 5.4 2.5 - - - +
435A THR* 4.1 9.9 - - + +
436A LYS* 1.3 78.2 - - - +
438A VAL* 1.3 68.6 + - - +
439A VAL* 4.9 3.1 - - + -
465A CYS 3.4 22.7 - - - +
466A VAL* 3.8 15.7 - - + -
467A ASN* 2.8 36.4 + - - +
468A ARG 3.3 5.9 + - - +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 3.8 7.2 - - + +
396A LEU* 3.3 26.5 - - + -
397A THR 3.0 5.6 + - - +
398A MET* 3.3 21.2 - - + +
399A LEU* 3.0 25.1 + - - +
436A LYS* 3.7 21.3 - - - -
437A VAL* 1.3 77.2 - - - +
439A VAL* 1.3 66.7 - - - +
440A THR* 4.7 1.3 - - + -
468A ARG* 3.4 20.2 - - + +
470A ILE* 3.6 31.9 - - + -
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU* 3.2 14.1 - - + +
400A GLY 4.5 1.6 - - - +
401A ALA* 3.5 24.2 - - + -
404A VAL* 3.8 13.0 - - + -
410A LEU* 3.8 29.4 - - + -
437A VAL* 4.1 2.4 - - + -
438A VAL* 1.3 74.9 - - - +
440A THR* 1.3 64.3 + - - +
441A MET* 3.9 17.3 - - + -
466A VAL* 3.9 19.7 - - + -
468A ARG 2.9 13.0 + - - +
469A ILE* 4.4 4.5 - - + -
470A ILE* 2.8 29.3 + - - +
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Residues in contact with THR 440 (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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305A ILE* 3.7 16.8 - - + -
309A ALA* 3.7 25.4 - - + -
325A ILE* 3.8 15.4 - - + +
326A PRO* 3.6 23.1 - - + +
398A MET* 3.7 24.5 - - + -
399A LEU 2.9 11.4 + - - -
400A GLY* 3.6 17.0 - - - -
438A VAL* 4.7 0.9 - - + -
439A VAL* 1.3 74.5 - - - +
441A MET* 1.3 62.5 + - - +
470A ILE* 3.5 13.2 - - + -
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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