Contacts of the strand formed by residues 401 - 410 (chain C) in PDB entry 2Q7N
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 VAL 401 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C VAL* 3.7 19.5 - - + -
394C LYS 3.5 7.4 - - - +
395C ASP* 3.8 21.3 - - + -
396C ILE* 4.0 8.8 - - - +
397C ASN 4.6 3.1 - - - +
400C VAL* 1.3 79.8 - - - +
402C THR* 1.3 59.7 + - - +
447C ALA* 3.8 2.6 - - - -
448C VAL* 2.8 56.2 + - + +
451C LEU* 3.8 26.5 - - + -
459C PHE* 4.3 9.9 - - + -
480C HIS* 4.3 9.6 - - + +
482C THR* 4.9 9.4 - - + -
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Residues in contact with THR 402 (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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392C LYS 3.5 1.0 - - - +
393C VAL* 3.2 8.9 - - - -
394C LYS* 2.7 43.3 + - + +
396C ILE* 3.7 23.7 - - - +
401C VAL* 1.3 70.4 + - - +
403C PHE* 1.3 68.0 + - - +
404C SER* 3.8 7.4 + - - +
445C HIS* 5.1 14.5 - - + +
446C VAL 3.8 10.0 + - - +
447C ALA* 4.5 4.5 - - - +
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Residues in contact with PHE 403 (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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391C LEU* 3.3 37.9 - - + -
392C LYS 3.7 2.7 - - - -
393C VAL* 3.6 18.8 - - + +
401C VAL* 4.0 2.4 + - - +
402C THR* 1.3 73.9 - - - +
404C SER* 1.3 78.8 + - - +
405C TRP* 3.5 21.1 - + - -
420C ILE* 3.9 10.8 - - + -
445C HIS* 4.0 0.2 - - - -
446C VAL* 3.0 37.0 + - + +
448C VAL* 4.0 14.8 - - + -
459C PHE* 3.3 39.7 - + + -
460C ARG 4.1 3.8 - - - -
461C VAL* 2.9 35.7 - - + -
478C LYS* 5.2 1.1 - - + -
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Residues in contact with SER 404 (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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390C SER 3.8 2.1 - - - +
391C LEU* 3.2 4.6 - - - -
392C LYS* 2.8 48.6 + - - +
394C LYS 5.4 0.3 + - - -
402C THR* 3.8 7.5 + - - +
403C PHE* 1.3 84.7 - - - +
405C TRP* 1.3 64.4 + - - +
443C THR* 5.2 4.9 - - - -
444C TYR 3.1 15.9 - - - -
445C HIS* 3.5 20.5 + - - -
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Residues in contact with TRP 405 (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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388C PRO* 3.5 24.2 - - + -
389C THR 3.7 5.2 - - - +
390C SER 4.9 0.7 - - - -
391C LEU* 3.6 26.2 - - + -
403C PHE* 3.5 17.9 - + - -
404C SER* 1.3 83.1 - - - +
406C TYR* 1.3 63.3 + - - +
407C LEU* 3.9 8.1 + - + +
418C CYS* 3.4 32.5 - - + -
420C ILE* 4.9 0.9 - - + -
436C ILE* 4.8 5.6 - - + -
443C THR* 3.8 7.9 - - - +
444C TYR* 3.2 52.0 + + + +
446C VAL* 3.5 36.3 - - + -
461C VAL* 3.6 12.8 - - + -
463C CYS* 3.0 20.7 - - - -
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Residues in contact with TYR 406 (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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388C PRO* 3.5 5.0 - - - +
389C THR* 3.0 45.1 + - - +
390C SER* 4.7 8.5 - - - +
405C TRP* 1.3 69.1 - - - +
407C LEU* 1.3 82.5 + - - +
408C PRO* 3.7 32.3 - - + +
441C ASP* 4.2 26.9 + - + +
442C SER 5.0 2.0 - - - -
443C THR* 3.8 31.1 - - + +
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Residues in contact with LEU 407 (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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385C PRO* 4.4 5.8 - - + -
386C HIS 3.8 35.0 - - - +
387C ASP 4.5 0.9 - - - +
388C PRO* 4.0 11.0 - - + -
405C TRP* 3.9 6.7 - - + +
406C TYR* 1.3 81.9 - - - +
408C PRO* 1.3 78.0 - - + +
409C GLY 3.7 1.4 + - - -
411C PHE* 3.9 11.2 - - + -
416C LEU* 4.2 10.3 - - + -
442C SER 3.6 15.7 + - - +
444C TYR* 3.9 31.5 + - + -
463C CYS* 3.2 44.2 - - + +
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Residues in contact with PRO 408 (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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296C HIS 4.4 1.9 - - - +
297C ASP* 4.2 10.5 - - + +
386C HIS* 4.7 24.2 + - + +
387C ASP 5.1 5.8 - - - +
389C THR* 5.3 4.0 - - - +
406C TYR* 3.7 26.5 - - + +
407C LEU* 1.3 95.7 - - + +
409C GLY* 1.4 56.5 + - - +
411C PHE* 3.0 15.0 - - - -
441C ASP* 3.5 12.8 - - - +
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Residues in contact with GLY 409 (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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297C ASP* 3.9 19.5 - - - +
298C LEU 3.9 2.2 - - - -
299C LYS* 5.4 1.8 - - - -
407C LEU 3.7 1.0 + - - -
408C PRO* 1.4 70.3 - - - +
410C ASN* 1.3 54.6 + - - -
411C PHE* 2.6 36.7 + - - -
439C ALA 3.0 10.2 - - - +
441C ASP* 2.9 22.9 + - - -
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Residues in contact with ASN 410 (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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298C LEU* 3.2 42.6 - - + +
299C LYS* 4.8 13.1 - - + +
353C PRO* 5.9 0.2 - - - +
409C GLY* 1.3 62.9 - - - -
411C PHE* 1.3 60.2 + - - +
412C THR* 3.6 15.1 + - - -
413C LYS* 4.5 4.7 + - - +
440C GLU* 2.8 26.5 + - + +
441C ASP* 4.7 2.6 + - - -
1S NAG 1.5 67.2 + - - +
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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