Contacts of the strand formed by residues 437 - 444 (chain B) in PDB entry 3C7N
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 GLY 437 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435B GLN* 3.5 4.3 - - - +
436B PRO* 1.3 84.8 - - - +
438B VAL* 1.3 61.9 + - - -
461B LEU 2.9 15.5 - - - -
462B THR* 3.9 7.0 - - - -
464B ILE* 3.4 9.6 - - - -
543B GLU* 3.0 28.6 - - - +
544B SER* 3.8 7.0 + - - -
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Residues in contact with VAL 438 (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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429B THR 4.7 3.4 - - - +
430B THR* 5.1 0.9 - - - -
435B GLN* 3.6 19.7 - - - +
437B GLY* 1.3 73.7 - - - -
439B LEU* 1.3 59.5 + - - +
440B ILE* 3.9 14.4 + - + -
460B GLU* 3.6 7.1 - - - +
461B LEU* 2.8 58.6 + - + +
464B ILE* 4.1 9.4 - - + -
474B ILE* 4.1 22.0 - - + -
541B SER* 3.6 28.3 - - - +
542B LEU 3.9 2.9 - - - -
544B SER* 4.1 2.9 - - - -
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLU 5.0 5.5 - - - +
438B VAL* 1.3 72.4 - - - +
440B ILE* 1.3 67.8 + - - +
441B GLN* 3.4 21.5 + - + +
458B LYS* 4.3 16.8 - - + -
459B PHE 3.3 24.9 - - - +
460B GLU* 4.6 9.0 - - + +
541B SER* 4.8 9.2 - - - -
542B LEU 3.2 13.7 + - - +
544B SER* 3.2 26.7 - - - +
545B TYR 4.5 0.7 - - - +
546B ALA* 3.4 41.5 - - + +
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Residues in contact with ILE 440 (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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403B ILE* 4.2 14.4 - - + -
404B GLU 6.0 0.4 - - - -
438B VAL* 4.1 24.2 - - + +
439B LEU* 1.3 72.0 - - - +
441B GLN* 1.3 59.8 + - - +
442B VAL* 4.1 15.5 - - + -
458B LYS* 3.3 4.9 - - - +
459B PHE* 3.0 66.2 + - + +
461B LEU* 4.9 2.0 - - + +
474B ILE* 4.9 2.0 - - + -
476B VAL* 4.2 21.3 - - + -
488B VAL* 4.1 6.5 - - + -
490B ALA* 3.5 29.8 - - + -
541B SER* 5.3 6.1 - - - +
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Residues in contact with GLN 441 (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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403B ILE* 3.1 8.3 - - - +
404B GLU* 3.1 61.4 + - + +
439B LEU* 3.4 28.7 + - + +
440B ILE* 1.3 75.6 - - - +
442B VAL* 1.3 62.7 + - - +
443B TYR* 3.5 27.2 + - + -
455B LEU* 4.2 11.8 - - + +
457B GLY 3.8 4.3 - - - -
458B LYS* 4.2 13.4 - - + +
545B TYR 5.3 0.6 + - - -
546B ALA* 3.8 17.2 - - - +
547B PHE* 3.9 15.8 + - - +
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Residues in contact with VAL 442 (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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401B LEU* 5.3 0.9 - - + -
402B GLY 3.5 3.6 - - - +
403B ILE* 4.4 2.7 - - + -
440B ILE* 4.1 9.6 - - + -
441B GLN* 1.3 71.1 - - - +
443B TYR* 1.3 63.6 + - - +
455B LEU* 3.4 5.9 - - - +
456B LEU* 3.0 36.4 + - + +
457B GLY 3.0 20.6 + - - +
459B PHE* 4.8 3.4 - - + -
478B PHE* 3.8 25.6 - - + -
486B LEU* 4.5 10.8 - - + -
488B VAL* 3.5 39.5 - - + -
501B ILE* 5.1 0.2 - - + -
503B ILE* 4.4 9.4 - - + -
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Residues in contact with TYR 443 (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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401B LEU* 3.6 4.0 - - - +
402B GLY 2.6 36.8 + - - +
404B GLU* 3.6 23.5 + - + -
410B MET* 3.4 23.9 - - - +
441B GLN* 3.5 44.0 + - + -
442B VAL* 1.3 75.9 - - - +
444B GLU* 1.3 59.0 + - - +
450B THR* 3.1 41.8 + - + -
453B ASN* 3.9 5.8 - - + -
454B ASN 3.4 21.3 - - - -
455B LEU* 3.7 30.6 - - + +
456B LEU* 4.8 3.1 - - - -
547B PHE* 5.3 8.3 - - - -
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Residues in contact with GLU 444 (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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398B PRO* 4.1 10.0 - - - +
399B LEU* 3.2 52.1 + - + +
400B SER 3.5 7.2 - - - +
401B LEU* 3.7 22.2 - - + +
443B TYR* 1.3 74.8 - - - +
445B GLY* 1.3 57.6 + - - +
453B ASN* 3.7 3.0 - - - -
454B ASN* 2.8 42.0 + - + +
456B LEU* 3.8 26.6 - - + +
510B LEU* 6.0 0.3 - - - +
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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