Contacts of the strand formed by residues 328 - 335 (chain P) in PDB entry 1SVC
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 ALA 328 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263P VAL* 6.2 0.2 - - + -
287P GLU* 4.1 6.7 - - - +
319P TYR* 3.3 37.9 - - + +
324P ILE* 5.7 4.9 - - + -
326P LYS 4.0 1.3 + - - +
327P PRO* 1.3 73.0 - - - +
329P SER* 1.3 60.7 + - - +
330P VAL 3.6 2.1 + - - -
349P LEU* 3.8 2.9 - - - -
350P TYR* 2.9 41.0 + - + +
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Residues in contact with SER 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287P GLU* 3.6 16.0 + - - +
327P PRO 4.3 0.6 + - - -
328P ALA* 1.3 70.5 - - - +
330P VAL* 1.3 62.7 + - - +
331P PHE* 5.5 3.3 - - - -
348P PHE 3.5 9.2 - - - -
349P LEU* 3.3 18.4 - - - +
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Residues in contact with VAL 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285P PHE* 4.4 8.3 - - + -
286P TYR 3.4 11.7 - - - +
287P GLU* 3.7 24.0 - - + +
295P TRP* 3.6 23.8 - - + -
319P TYR* 3.9 12.1 - - + -
328P ALA 4.4 1.3 - - - +
329P SER* 1.3 80.4 - - - +
331P PHE* 1.3 75.6 + - - +
347P PRO* 4.0 1.0 - - - +
348P PHE* 2.9 45.1 + - + +
350P TYR* 3.4 27.6 - - + -
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Residues in contact with PHE 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284P ARG 3.4 1.4 - - - +
285P PHE* 2.9 9.7 - - - +
286P TYR* 2.7 76.9 + + + +
287P GLU* 5.4 2.9 - - - -
288P GLU* 5.8 1.8 - - + -
329P SER 5.5 3.1 - - - -
330P VAL* 1.3 82.5 - - - +
332P VAL* 1.3 63.1 - - - +
345P PRO* 3.6 22.4 - - + -
346P LYS 3.3 16.8 - - - -
347P PRO* 4.6 14.4 - - + -
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Residues in contact with VAL 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253P ILE* 3.7 17.4 - - + +
256P MET* 4.1 24.0 - - + -
271P LEU* 4.5 1.1 - - + -
283P ILE* 4.0 21.1 - - + -
284P ARG 3.3 4.0 - - - +
285P PHE* 3.2 39.3 - - + -
314P PHE* 5.2 0.4 - - + -
331P PHE* 1.3 73.8 - - - +
333P GLN* 1.3 66.2 + - - +
345P PRO* 3.5 0.3 - - - +
346P LYS* 2.7 42.2 + - + +
348P PHE* 3.7 20.4 - - + -
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Residues in contact with GLN 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253P ILE* 3.6 11.2 - - - -
283P ILE* 3.5 2.8 - - - -
284P ARG* 2.7 71.1 + - + +
286P TYR* 3.4 28.7 + - + -
332P VAL* 1.3 80.3 - - - +
334P LEU* 1.3 62.1 + - - +
342P THR* 3.3 30.6 + - - +
343P SER* 3.3 26.7 + - - +
345P PRO* 4.1 10.7 - - + +
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Residues in contact with LEU 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251P LEU* 4.5 7.9 - - + -
252P LYS 3.6 40.6 - - - +
253P ILE* 3.6 10.8 - - + -
271P LEU* 4.1 21.5 - - + -
273P CYS* 3.7 14.4 - - + -
274P ASP 5.1 0.4 - - - +
276P VAL* 4.7 8.7 - - + -
281P ILE* 4.1 16.6 - - + -
282P GLN 3.3 11.7 - - - +
283P ILE* 4.2 15.3 - - + -
312P ILE* 4.5 7.2 - - + -
333P GLN* 1.3 75.6 - - - +
335P ARG* 1.3 61.0 + - - +
342P THR* 3.4 6.8 - - - +
343P SER* 2.9 28.8 + - - +
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Residues in contact with ARG 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251P LEU* 4.4 2.0 - - - -
281P ILE* 3.6 3.7 - - - -
282P GLN* 2.8 72.6 + - + +
284P ARG* 3.5 41.9 - - + +
296P GLU* 3.6 12.3 + - - -
298P PHE* 3.8 13.5 - - - -
334P LEU* 1.3 75.5 - - - +
336P ARG* 1.3 64.5 + - - +
337P LYS 3.6 0.5 + - - -
340P LEU* 3.3 38.8 - - + +
341P GLU 3.4 3.8 - - - -
342P THR* 3.5 21.8 - - + -
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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