Contacts of the strand formed by residues 360 - 368 (chain C) in PDB entry 3Q41
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 360 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C LEU* 3.6 3.1 - - - -
357C GLN* 2.8 36.0 + - - +
358C ASN* 3.9 12.3 - - - +
359C ARG* 1.3 83.0 - - + +
361C LEU* 1.3 64.5 + - - +
362C VAL* 3.4 14.0 + - + +
377C ARG* 5.2 10.1 - - - +
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Residues in contact with LEU 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ILE* 3.9 34.5 - - + +
259C LEU* 3.8 24.9 - - + -
266C ILE* 5.6 0.9 - - + +
268C GLY 5.5 0.4 - - - +
270C GLN* 4.6 9.2 - - - +
354C MET* 3.3 44.3 - - + +
355C ASN 3.5 10.3 - - - +
356C LEU* 3.8 22.2 - - + +
359C ARG 4.2 0.4 + - - -
360C LYS* 1.3 71.2 - - - +
362C VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C MET* 3.3 6.7 - - - -
355C ASN 2.8 43.2 + - - +
357C GLN* 3.4 37.5 - - + +
360C LYS* 3.4 18.6 + - + +
361C LEU* 1.3 76.6 - - - +
363C GLN* 1.3 59.9 + - - +
364C VAL* 4.0 13.2 - - + -
377C ARG* 4.0 39.3 - - - +
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Residues in contact with GLN 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 5.4 0.6 - - - +
352C SER* 3.3 26.5 + - - +
353C ILE 3.6 3.8 - - - +
354C MET* 3.8 9.6 - - + +
361C LEU 4.3 0.2 + - - -
362C VAL* 1.3 74.6 - - - +
364C VAL* 1.3 62.3 + - - +
365C GLY 3.5 12.6 - - - +
366C ILE* 3.6 38.2 - - - +
375C ASN* 3.6 19.5 + - - +
377C ARG* 4.3 11.3 - - - +
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Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C TYR* 5.0 4.5 + - - +
267C ILE* 4.9 0.7 - - + -
353C ILE* 3.2 24.9 + - + +
355C ASN* 3.5 42.2 - - + +
362C VAL* 4.0 10.3 - - + -
363C GLN* 1.3 76.9 - - - +
365C GLY* 1.3 60.4 + - - +
374C PRO* 3.5 5.4 - - - +
375C ASN* 2.9 35.8 + - - +
377C ARG* 4.1 16.8 - - + +
378C LYS 4.3 7.0 - - - +
379C ILE* 4.2 22.7 - - + -
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Residues in contact with GLY 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C TYR* 5.9 0.7 - - - -
353C ILE* 2.8 41.1 + - - +
363C GLN* 3.5 12.2 + - - +
364C VAL* 1.3 85.4 - - - +
366C ILE* 1.3 61.8 + - - +
372C VAL* 5.4 1.6 - - - -
373C ILE 3.7 11.4 - - - -
374C PRO* 4.0 4.9 - - - -
375C ASN* 5.0 1.8 - - - -
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Residues in contact with ILE 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ILE* 4.0 20.9 - - + -
350C ASN* 4.9 11.7 - - + +
351C TYR 3.9 9.6 - - - +
353C ILE* 3.6 3.7 - - - +
363C GLN* 3.6 19.5 - - - +
365C GLY* 1.3 74.6 - - - -
367C TYR* 1.3 67.9 + - - +
368C ASN* 4.2 1.5 + - + +
371C HIS 4.1 0.9 - - - +
373C ILE* 2.9 59.6 + - + +
374C PRO 5.5 0.2 - - - +
375C ASN* 6.0 4.9 - - + +
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Residues in contact with TYR 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C SER* 4.1 18.4 + - - -
150C VAL* 3.8 27.4 - - + -
153C GLU* 4.2 12.1 - - + +
348C PHE* 4.2 6.2 - + - -
350C ASN* 3.1 6.1 - - - +
351C TYR* 2.8 76.7 + + + +
353C ILE* 3.6 15.7 - - + +
366C ILE* 1.3 75.9 - - - +
368C ASN* 1.3 58.5 + - - +
369C GLY* 3.4 19.7 + - - -
370C THR* 3.4 38.6 + - - -
371C HIS 3.2 22.7 - - - -
372C VAL* 3.7 11.9 - - + -
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Residues in contact with ASN 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ASN* 3.5 24.9 - - - +
366C ILE* 4.2 1.9 - - + +
367C TYR* 1.3 77.6 - - - +
369C GLY* 1.3 50.5 - - - +
370C THR* 2.1 29.0 + - - +
371C HIS 3.1 15.6 + - - +
373C ILE* 4.9 5.1 - - - +
409C NAG 1.4 69.0 + - + +
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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