Contacts of the strand formed by residues 415 - 422 (chain A) in PDB entry 4CCN
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 SER 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A TYR 4.3 0.4 - - - -
329A LEU* 3.3 7.6 - - - +
330A THR 2.8 33.3 + - - -
350A GLN* 2.9 22.6 + - - -
352A GLU 3.5 5.4 - - - -
354A ARG 3.3 17.5 - - - -
355A LYS* 3.3 24.4 - - - +
409A CYS* 3.3 12.6 - - - -
414A HIS* 1.3 79.4 - - - +
416A LEU* 1.3 62.1 + - - +
417A HIS* 4.5 2.3 + - - -
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Residues in contact with LEU 416 (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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242A PHE* 4.7 2.0 - - + -
243A SER* 3.6 12.6 - - - +
244A THR* 3.4 38.1 - - - +
247A LEU* 5.2 3.8 - - + -
327A VAL* 3.7 17.0 - - + -
328A TYR 3.3 14.6 - - - +
329A LEU* 3.7 26.5 - - + -
350A GLN* 3.8 1.0 + - - -
351A LEU* 2.8 40.9 + - + +
352A GLU* 2.9 36.2 + - + +
414A HIS* 4.7 0.7 - - + -
415A SER* 1.3 77.6 + - - +
417A HIS* 1.3 62.7 + - - +
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Residues in contact with HIS 417 (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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327A VAL* 3.5 5.0 - - - +
328A TYR* 2.8 55.3 + + + +
348A VAL* 3.5 16.4 - - + -
349A LEU 3.0 19.1 - - - +
350A GLN* 3.6 16.2 + - - +
351A LEU* 3.9 7.2 - - - -
355A LYS* 4.1 13.9 + - - +
357A TRP* 3.7 12.8 + + - -
415A SER* 4.5 1.0 + - - -
416A LEU* 1.3 76.5 - - - +
418A LEU* 1.3 58.7 + - - +
419A THR* 3.2 16.9 + - - -
902A OGA 2.8 49.6 + - - -
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Residues in contact with LEU 418 (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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241A LEU* 4.6 14.4 - - + -
242A PHE* 4.8 4.5 - - + -
308A VAL* 4.1 33.9 - - + -
311A PHE* 5.5 5.4 - - + -
312A LEU* 5.9 0.9 - - + -
325A SER* 4.3 11.2 - - - +
326A ASN 3.5 9.2 - - - +
327A VAL* 4.2 15.9 - - + +
347A PHE 3.6 1.0 - - - +
349A LEU* 2.8 45.8 + - + +
351A LEU* 4.0 18.1 - - + +
417A HIS* 1.3 73.9 - - - +
419A THR* 1.3 63.7 + - - +
420A LEU* 3.8 24.0 - - + +
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Residues in contact with THR 419 (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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325A SER* 3.2 4.7 - - - -
326A ASN 2.8 30.3 + - - -
328A TYR* 3.5 14.1 - - - -
342A ASP* 6.0 0.2 - - - +
344A ILE* 5.5 0.2 - - + -
346A ALA* 4.1 18.2 - - + -
347A PHE 3.5 5.4 - - - +
348A VAL* 3.4 7.5 - - + +
417A HIS* 3.2 11.9 + - - -
418A LEU* 1.3 71.7 - - - +
420A LEU* 1.3 68.7 + - - +
421A SER* 4.7 0.7 - - - -
902A OGA 2.6 31.2 + - - +
216C HIS* 3.5 23.5 - - + +
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Residues in contact with LEU 420 (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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209A LEU* 3.7 21.8 - - + -
311A PHE* 4.5 7.2 - - + -
312A LEU* 3.4 29.6 - - + -
315A LEU* 3.7 26.2 - - + -
319A PHE* 4.6 9.4 - - + -
323A ALA* 4.0 10.8 - - + -
324A GLY 3.5 6.1 - - - +
325A SER* 4.5 0.2 - - - -
345A GLU 3.7 0.3 - - - +
346A ALA* 3.4 2.9 - - - -
347A PHE* 2.7 54.9 + - + +
349A LEU* 4.5 3.4 - - + -
418A LEU* 3.7 15.3 + - + +
419A THR* 1.3 74.3 - - - +
421A SER* 1.3 74.0 + - - +
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Residues in contact with SER 421 (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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323A ALA* 3.3 2.9 - - - -
324A GLY 2.8 33.8 + - - +
344A ILE* 3.5 24.5 - - - -
345A GLU 3.1 5.6 - - - -
347A PHE* 5.5 0.2 - - - -
419A THR* 3.7 1.5 + - - -
420A LEU* 1.3 78.4 - - - +
422A THR* 1.3 66.3 + - - +
216C HIS* 2.8 32.7 + - - -
218C HIS* 2.9 17.6 + - - -
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Residues in contact with THR 422 (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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223A TRP* 3.9 27.4 - - + -
319A PHE* 4.0 32.2 - - + +
321A SER* 3.6 17.2 + - - -
322A MET 2.9 20.5 + - - -
323A ALA* 4.3 0.7 - - - -
344A ILE* 3.0 7.0 - - - +
345A GLU* 3.0 30.7 + - + +
347A PHE* 4.7 3.1 - - + -
421A SER* 1.3 79.3 - - - +
423A TYR* 1.3 73.6 + - + +
424A GLN 3.5 2.5 - - - -
218C HIS* 3.9 4.3 - - - -
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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