Contacts of the strand formed by residues 315 - 321 (chain D) in PDB entry 2HVH
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 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A ARG* 4.1 9.4 - - - +
313D ALA* 3.2 6.9 + - - +
314D ASP* 1.3 84.7 + - - +
316D ALA* 1.3 70.2 + - - +
339D ASN* 3.3 19.6 - - - +
340D GLU* 4.7 1.0 + - - +
367D LYS* 3.2 24.2 + - + +
369D SER* 3.7 13.7 - - - +
391D SER* 4.7 6.2 + - - -
455D TRP* 3.8 29.0 - - + -
458D GLU* 3.1 35.4 + - - -
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D MET 5.4 0.2 - - - +
313D ALA 5.0 1.6 - - - +
315D LYS* 1.3 78.2 - - - +
317D ALA* 1.3 55.5 + - - +
337D VAL* 3.9 17.7 - - + -
338D VAL 3.3 11.7 - - - +
339D ASN* 3.9 5.8 - - + +
360D TRP* 3.9 27.8 - - + -
367D LYS 3.1 6.3 + - - +
368D LYS* 3.3 4.9 - - - -
369D SER* 2.7 32.6 + - - -
455D TRP* 3.7 8.1 - - - -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ALA* 1.3 73.6 - - - +
318D LEU* 1.3 59.1 + - - +
336D ALA 3.7 0.9 - - - +
337D VAL* 3.3 7.8 - - - +
338D VAL* 2.7 38.0 + - + +
369D SER* 3.3 9.9 - - - +
451D ALA* 3.2 33.4 - - - +
454D ILE* 4.2 5.6 - - + -
455D TRP* 3.6 23.3 - - + +
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ALA 3.8 0.4 + - - -
317D ALA* 1.3 74.8 - - - +
319D VAL* 1.3 77.2 + - - +
320D VAL* 4.1 13.7 - - + -
335D ILE* 4.3 6.7 - - + -
336D ALA 3.6 10.1 - - - +
337D VAL* 3.9 17.7 - - + -
357D PHE* 4.5 3.6 - - + -
360D TRP* 4.0 17.0 - - + -
361D LEU* 3.9 24.2 - - + -
368D LYS* 4.1 21.8 - - + -
369D SER 2.7 14.1 + - - +
370D MET* 3.5 49.2 - - + +
371D PHE 4.7 0.5 + - - -
387D LEU* 4.4 4.5 - - + -
451D ALA* 5.5 0.2 - - - +
454D ILE* 4.6 1.3 - - - +
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Residues in contact with VAL 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D LEU* 1.3 78.7 - - - +
320D VAL* 1.3 63.9 + - - +
321D GLU* 3.7 26.2 - - + +
335D ILE* 3.3 11.8 - - - +
336D ALA* 3.0 39.5 + - + +
370D MET* 4.8 0.7 - - - -
447D LEU* 4.1 23.6 - - + +
450D LYS* 4.3 10.5 - - + -
451D ALA* 3.8 31.6 - - + +
454D ILE* 4.2 12.1 - - + -
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Residues in contact with VAL 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D LEU* 4.1 26.6 + - + -
319D VAL* 1.3 76.1 - - - +
321D GLU* 1.3 61.9 + - - +
322D VAL* 3.5 9.9 + - + +
332D ILE* 3.7 40.2 - - + -
334D GLY 3.8 2.9 - - - +
335D ILE* 4.8 11.7 - - + -
352D LEU* 5.8 0.9 - - + -
357D PHE* 6.2 0.9 - - + -
361D LEU* 5.4 3.1 - - + -
370D MET* 4.4 4.6 - - + +
375D ARG* 5.6 2.3 - - - +
376D ALA* 3.8 30.4 + - + +
380D LEU* 4.4 20.0 - - + -
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Residues in contact with GLU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D VAL* 3.7 13.0 - - + +
320D VAL* 1.3 71.7 - - - +
322D VAL* 1.3 65.1 + - - +
323D VAL* 4.2 6.8 - - + +
332D ILE* 3.5 3.7 - - - +
333D VAL* 2.8 45.4 + - + +
334D GLY 2.9 19.7 + - - +
425D ASP* 4.7 0.7 - - - -
429D TYR* 2.5 35.8 + - - +
447D LEU* 3.5 20.6 - - + -
450D LYS* 2.7 29.9 + - - -
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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