Contacts of the strand formed by residues 411 - 421 (chain S) in PDB entry 6O81
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 LEU 411 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257S ILE* 5.6 0.6 - - - +
355S GLY* 5.0 22.9 - - - +
406S VAL 3.2 4.7 - - - +
407S ASN* 4.3 0.9 - - - -
408S ILE* 2.9 43.1 + - + +
409S GLY 3.5 0.2 - - - -
410S SER* 1.3 74.0 - - - +
412S SER* 1.3 59.8 + - - +
413S THR* 3.6 4.1 + - - -
433S VAL* 5.3 12.8 - - + -
434S CYS 6.1 2.5 - - - +
435S THR* 5.9 3.8 - - - -
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Residues in contact with SER 412 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 5.0 3.5 - - - -
79S ILE* 5.4 13.2 - - - -
355S GLY* 6.0 0.8 - - - -
405S MET* 3.9 25.3 - - - +
406S VAL 3.4 5.8 - - - -
407S ASN* 4.1 11.7 - - - +
410S SER 3.4 7.1 + - - -
411S LEU* 1.3 70.1 - - - +
413S THR* 1.3 60.0 + - - +
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Residues in contact with THR 413 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 4.8 3.4 - - - -
405S MET* 3.7 4.0 - - - -
406S VAL* 2.9 39.1 + - - +
411S LEU* 3.6 4.7 + - - -
412S SER* 1.3 73.7 - - - +
414S GLY* 1.3 65.8 + - - +
429S LEU* 5.0 5.4 - - - -
431S ASN* 4.9 19.5 - - - -
433S VAL* 4.9 18.2 - - - -
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Residues in contact with GLY 414 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 3.5 43.2 - - - -
403S VAL* 6.2 0.2 - - - -
404S LEU 3.4 8.1 - - - -
405S MET* 3.8 5.1 - - - -
413S THR* 1.3 75.0 - - - +
415S GLY* 1.3 58.4 + - - -
429S LEU* 3.6 4.4 - - - +
430S THR* 2.9 27.6 + - - -
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Residues in contact with GLY 415 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 5.3 1.4 - - - +
402S GLU 3.5 2.1 - - - +
403S VAL* 3.5 3.3 - - - +
404S LEU* 2.9 37.4 + - - +
406S VAL* 5.9 1.5 - - - +
413S THR 3.9 0.2 + - - -
414S GLY* 1.3 74.5 - - - -
416S ARG* 1.3 61.8 + - - -
417S VAL 4.0 0.2 + - - -
427S ILE* 4.9 9.1 - - - +
428S VAL 3.3 13.5 - - - -
429S LEU* 3.8 6.3 - - - -
430S THR* 4.4 0.9 - - - -
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Residues in contact with ARG 416 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401S ASN* 4.8 6.5 - - + -
402S GLU 3.4 14.4 - - - +
403S VAL* 4.5 2.0 - - + +
415S GLY* 1.3 72.4 - - - -
417S VAL* 1.3 61.2 + - - +
418S SER* 3.1 5.9 + - - +
427S ILE* 3.3 3.2 - - - -
428S VAL* 2.9 39.0 + - + +
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Residues in contact with VAL 417 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398S LEU* 5.0 12.6 - - + +
399S SER 3.4 21.3 - - - +
400S LYS* 3.6 3.3 - - - -
401S ASN* 2.9 25.0 + - - -
402S GLU* 3.0 18.5 + - + +
416S ARG* 1.3 68.2 - - - +
418S SER* 1.3 64.8 + - - +
419S ALA 3.5 5.4 - - - +
420S VAL* 5.9 2.9 - - + -
426S LYS 4.3 4.0 - - - -
427S ILE* 4.5 5.6 - - + +
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Residues in contact with SER 418 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400S LYS* 4.8 8.7 - - - +
401S ASN* 5.8 0.2 - - - +
416S ARG* 3.1 10.8 + - - -
417S VAL* 1.3 74.3 - - - +
419S ALA* 1.3 62.8 + - - +
426S LYS* 3.2 15.0 + - - -
428S VAL* 4.7 13.2 - - - -
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Residues in contact with ALA 419 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400S LYS* 6.3 0.2 - - - -
417S VAL* 4.9 4.6 - - - +
418S SER* 1.3 82.3 + - - +
420S VAL* 1.3 64.1 + - - +
424S LEU 4.6 0.2 - - - -
425S GLY* 3.5 0.9 - - - -
426S LYS* 2.9 38.3 + - + +
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Residues in contact with VAL 420 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398S LEU* 4.3 26.9 - - + +
417S VAL* 5.9 3.1 - - + -
419S ALA* 1.3 78.1 - - - +
421S LYS* 1.3 60.0 + - - +
422S ALA 3.9 3.7 + - - +
424S LEU 3.3 9.4 - - - +
425S GLY* 4.4 7.0 - - - -
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Residues in contact with LYS 421 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420S VAL* 1.3 72.8 - - - +
422S ALA* 1.3 56.7 + - + +
423S ASP* 2.5 19.3 + - - +
424S LEU* 2.9 24.3 + - + +
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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