Contacts of the strand formed by residues 331 - 336 (chain K) in PDB entry 6R90
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 331 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K THR 5.2 0.5 + - - -
15K VAL* 3.0 22.8 - - - +
35K LYS* 6.2 0.4 - - - -
323K PHE* 4.3 7.0 - - - -
324K VAL* 3.3 11.4 - - - -
325K GLY* 3.6 1.7 - - - -
326K SER 2.9 27.0 + - - +
329K GLY 3.5 1.4 + - - -
330K ASP* 1.3 76.5 - - - +
332K GLN* 1.3 64.2 + - - +
352K THR* 3.6 1.7 - - - -
353K PHE* 2.8 49.1 + - - -
354K THR 5.2 0.2 + - - -
355K ASN* 4.8 1.4 - - - +
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Residues in contact with GLN 332 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K GLU 5.7 0.4 + - - -
308K THR* 3.4 17.9 - - - +
309K SER* 3.0 38.7 + - - +
322K VAL 4.0 0.2 - - - +
323K PHE* 3.4 8.3 - - - -
324K VAL* 2.9 41.0 + - + +
330K ASP* 3.7 8.1 - - + +
331K SER* 1.3 82.1 - - - +
333K LEU* 1.3 60.9 + - - +
334K VAL* 4.1 16.6 - - + +
349K ALA* 4.8 15.3 - - + +
351K GLU 3.3 10.3 - - - +
352K THR* 5.1 9.7 + - + +
353K PHE* 3.6 6.9 - - - -
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Residues in contact with LEU 333 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K GLY* 3.9 18.4 - - - -
49K LEU* 3.8 23.3 - - + +
317K LEU* 4.3 12.3 - - + -
321K VAL* 4.5 6.7 - - + -
322K VAL 3.6 5.4 - - - +
323K PHE* 3.7 31.2 - - + -
332K GLN* 1.3 72.0 - - - +
334K VAL* 1.3 57.9 + - - +
349K ALA* 3.8 0.5 - - - -
350K MET* 2.7 41.8 + - + -
351K GLU* 2.9 47.3 + - + +
353K PHE* 3.6 19.0 - - + -
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Residues in contact with VAL 334 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280K LEU* 4.8 5.8 - - + -
308K THR* 4.8 3.8 - - + -
321K VAL* 3.4 4.3 - - - -
322K VAL* 2.9 56.4 + - + +
324K VAL* 4.4 12.6 - - + -
332K GLN* 4.2 24.5 - - + +
333K LEU* 1.3 77.7 - - - +
335K LYS* 1.3 58.9 + - - +
336K LEU* 4.6 9.6 - - + -
347K VAL* 4.0 24.2 - - + -
348K VAL 3.5 11.9 - - - +
349K ALA* 4.3 8.1 - - + -
350K MET* 3.4 9.4 - - - +
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Residues in contact with LYS 335 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K ALA 5.1 5.6 + - - -
47K GLU* 4.5 13.7 + - - -
319K ASN 5.3 3.8 - - - +
320K GLY 3.6 5.8 - - - +
321K VAL* 4.5 11.7 - - - +
334K VAL* 1.3 74.5 - - - +
336K LEU* 1.3 69.4 + - - +
337K ASN* 3.9 20.6 + - - +
346K TYR 3.6 5.0 - - - +
347K VAL* 3.9 2.6 - - - -
348K VAL* 3.0 35.8 + - + +
350K MET* 3.6 26.6 - - + +
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Residues in contact with LEU 336 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K VAL* 6.4 0.7 - - + -
272K LEU* 4.4 17.3 - - + -
280K LEU* 4.7 4.3 - - + -
282K MET* 5.7 7.0 - - + -
305K LEU* 4.5 21.1 - - + -
316K TYR* 4.4 8.1 - - + -
319K ASN 5.0 0.7 - - - +
320K GLY* 2.5 36.6 + - - +
322K VAL* 3.6 29.6 - - + -
334K VAL* 4.6 8.5 - - + -
335K LYS* 1.3 80.3 - - - +
337K ASN* 1.3 67.7 + - - +
338K VAL* 4.3 1.0 + - - +
346K TYR* 4.0 3.8 - - + +
347K VAL* 4.6 15.9 - - + -
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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