Contacts of the strand formed by residues 311 - 317 (chain H) in PDB entry 4P0S
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 THR 311 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G VAL* 4.6 16.8 - - + +
292H THR* 3.7 12.1 - - - +
293H TRP* 3.9 26.6 - - + -
309H GLU* 2.5 18.7 + - - +
310H PRO* 1.3 85.8 + - - +
312H VAL* 1.3 64.9 + - - +
357H LYS* 3.0 21.0 + - - +
358H ALA* 3.6 20.0 - - + +
439H PHE* 4.1 20.4 - - + -
443H VAL* 4.8 3.1 - - + +
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Residues in contact with VAL 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H VAL* 4.4 1.8 - - + -
290H SER* 4.2 9.4 - - - -
291H VAL 3.6 7.2 - - - +
292H THR* 3.8 19.7 - - + -
293H TRP* 4.5 0.2 - - - -
311H THR* 1.3 80.0 - - - +
313H LEU* 1.3 63.7 + - - +
314H VAL* 4.0 17.9 - - + -
350H ILE* 5.4 1.8 - - + -
354H THR* 3.7 25.6 - - + +
357H LYS* 3.3 32.1 - - + +
358H ALA 3.2 10.8 + - - +
359H LEU* 3.1 22.4 - - + +
360H SER 3.5 0.7 + - - -
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Residues in contact with LEU 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290H SER* 3.6 0.7 - - - -
291H VAL* 2.7 56.1 + - + +
293H TRP* 4.1 12.5 - - + -
312H VAL* 1.3 74.5 - - - +
314H VAL* 1.3 71.8 + - - +
315H LEU* 4.3 3.6 - - + +
360H SER* 3.1 26.9 - - - +
362H VAL* 4.1 16.4 - - + -
432H LEU* 6.6 0.4 - - + -
435H PHE* 4.1 13.0 - - + -
436H THR* 5.9 4.5 - - + +
439H PHE* 3.6 43.5 - - + -
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Residues in contact with VAL 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H VAL* 4.2 15.0 - - + -
288H PRO 4.9 1.6 - - - +
289H CYS 3.9 6.3 - - - +
290H SER* 3.8 18.6 - - - -
312H VAL* 4.0 8.1 - - + -
313H LEU* 1.3 79.2 - - - +
315H LEU* 1.4 66.7 + - - +
316H LEU* 5.4 0.2 - - + -
346H PHE* 4.8 7.9 - - + -
350H ILE* 4.1 23.1 - - + -
359H LEU* 3.4 23.6 - - + +
360H SER 2.9 16.0 + - - +
361H LEU* 2.8 41.3 - - + +
362H VAL 3.4 2.1 + - - -
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Residues in contact with LEU 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260H LEU* 3.7 15.5 - - + -
263H MET* 3.6 36.1 - - + -
269H LEU* 5.5 0.7 - - + -
289H CYS* 3.1 36.4 + - + +
291H VAL* 5.7 0.6 - - - +
313H LEU* 4.2 4.7 + - + +
314H VAL* 1.4 77.1 - - - +
316H LEU* 1.3 79.9 + - - +
317H ARG 3.9 2.5 - - - +
346H PHE* 6.0 0.3 - - - -
362H VAL* 3.8 11.9 - - + +
364H VAL* 3.8 16.4 - - + -
429H TRP* 4.3 1.3 - - + -
432H LEU* 3.5 42.4 - - + -
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Residues in contact with LEU 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289H CYS* 6.2 2.0 - - - -
314H VAL* 4.0 0.6 + - + -
315H LEU* 1.3 85.7 - - - +
317H ARG* 1.3 72.6 + - + +
320H ALA* 4.3 12.8 - - + -
321H PHE* 3.9 22.9 - - + +
324H MET* 3.6 28.3 - - + -
343H LEU* 6.1 0.9 - - + -
346H PHE* 4.3 24.5 - - + -
361H LEU* 3.9 31.9 - - + -
362H VAL 3.0 18.5 + - - +
363H ILE* 3.4 14.4 - - + +
364H VAL 3.6 3.1 + - - -
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Residues in contact with ARG 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263H MET* 3.2 42.4 - - - +
264H GLU* 3.0 37.3 + - - -
289H CYS* 6.0 2.5 - - - -
315H LEU* 3.9 3.8 + - - +
316H LEU* 1.3 82.0 - - + +
318H ALA* 1.3 71.2 + - + +
319H GLU* 3.6 34.3 - - + +
320H ALA* 3.2 17.6 + - + +
321H PHE* 3.4 8.5 + - - +
363H ILE* 4.5 0.2 - - - -
364H VAL* 4.3 10.8 + - + +
429H TRP* 4.3 8.3 - - - -
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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