Contacts of the strand formed by residues 337 - 348 (chain I) in PDB entry 5DST
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 GLN 337 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259I LEU 3.5 0.3 - - - +
260I VAL* 3.3 5.5 - - - +
261I ASP 2.9 32.4 + - - +
262I ILE* 3.4 9.4 - - - +
263I VAL* 2.9 32.3 + - + +
308I VAL* 3.6 18.2 - - + -
309I THR 3.9 7.4 - - - +
310I TYR* 4.4 2.0 - - + -
326I THR 2.4 33.8 + - - +
327I ALA 3.1 13.5 + - - -
328I PRO* 3.5 29.7 - - + +
335I TRP 4.1 1.3 - - - -
336I LYS* 1.3 85.9 + - - +
338I THR* 1.3 66.3 + - - +
339I VAL* 4.8 0.2 - - - -
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Residues in contact with THR 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I TYR* 4.2 3.3 - - - +
190I CYS* 3.1 37.5 + - + -
258I PRO* 3.9 17.0 - - + -
259I LEU 3.3 4.7 - - - +
260I VAL* 4.6 8.6 - - + +
308I VAL* 3.2 4.3 - - - -
309I THR* 2.9 46.0 + - - -
335I TRP 4.9 1.9 + - - -
337I GLN* 1.3 76.5 + - - +
339I VAL* 1.3 62.8 + - - +
340I PHE* 3.8 19.5 - - + -
393I MET* 4.2 9.2 - - - -
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Residues in contact with VAL 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ILE* 4.7 5.6 - - + -
228I ASP* 4.9 2.0 - - - +
258I PRO* 3.3 5.9 - - - +
259I LEU* 2.7 47.9 + - + +
261I ASP* 4.5 9.2 - - + +
263I VAL* 3.9 28.7 - - + -
306I ALA* 3.7 23.8 - - + -
307I LEU 3.6 4.0 - - - +
308I VAL* 4.0 8.1 - - + -
338I THR* 1.3 76.5 - - - +
340I PHE* 1.3 64.3 + - - +
341I TYR* 3.9 27.0 + - + +
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Residues in contact with PHE 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I CYS* 4.3 3.1 - - - -
258I PRO* 3.7 17.9 - - + -
306I ALA* 3.1 3.6 - - - +
307I LEU* 2.7 48.3 + - + +
309I THR* 3.8 28.0 - - + -
338I THR* 3.8 31.2 - - + -
339I VAL* 1.3 76.2 - - - +
341I TYR* 1.3 61.8 + - - +
342I LEU* 4.6 1.9 - - - +
358I ILE* 5.3 2.9 - - + -
372I PHE* 3.9 45.3 - + + -
374I VAL* 4.8 9.6 - - + -
391I TYR* 3.8 38.8 + + + +
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Residues in contact with TYR 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228I ASP* 2.7 30.6 + - + -
231I TYR* 3.4 19.1 - - - -
232I LYS* 3.5 41.0 + - + -
235I LYS* 4.8 1.3 - - + -
236I ILE* 4.1 20.0 - - + -
254I ALA 6.1 0.2 - - - -
255I MET* 3.9 31.3 + - - +
257I GLU 5.5 2.2 - - - -
258I PRO* 5.9 0.4 - - - +
259I LEU* 3.9 32.9 - - + +
305I HIS* 3.9 3.1 - - + -
306I ALA* 3.8 17.5 - - + -
339I VAL* 3.9 15.8 + - + +
340I PHE* 1.3 72.2 - - - +
342I LEU* 1.3 57.9 + - - +
389I ASN* 4.5 0.5 + - - -
391I TYR* 2.5 35.8 + - - -
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Residues in contact with LEU 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I LYS* 2.8 24.8 + - - -
255I MET* 3.5 6.9 - - - +
304I VAL* 4.1 32.3 - - + +
305I HIS 3.0 15.8 + - - +
306I ALA* 4.1 5.6 - - - +
307I LEU* 4.7 10.1 - - + -
340I PHE* 4.6 3.6 - - + +
341I TYR* 1.3 79.8 - - - +
343I GLU* 1.3 60.1 + - - +
344I ASP 3.5 15.7 - - - +
346I LEU* 4.2 19.3 - - + -
374I VAL* 5.7 2.9 - - + -
376I LEU* 4.2 24.9 - - + -
389I ASN* 4.2 12.6 - - - +
391I TYR* 4.2 9.6 - - - +
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Residues in contact with GLU 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I LYS* 3.3 13.7 + - - -
237I HIS* 5.2 4.5 - - - -
255I MET* 3.8 20.6 - - + +
256I LYS* 5.5 12.7 + - - -
342I LEU* 1.3 73.6 - - - +
344I ASP* 1.3 72.8 + - - +
387I VAL* 4.3 8.0 - - - +
389I ASN* 3.2 29.6 - - - +
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Residues in contact with ASP 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I LYS* 4.8 1.1 - - - +
342I LEU* 3.5 19.6 - - - +
343I GLU* 1.3 87.1 - - - +
345I TYR* 1.3 71.4 + - + +
346I LEU* 3.8 8.8 + - + +
385I THR* 5.8 7.4 - - + +
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Residues in contact with TYR 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I LYS* 4.9 4.7 - - - +
303I TYR* 3.7 33.9 - + - -
304I VAL 3.2 15.5 - - - +
305I HIS* 3.6 39.9 - + + +
344I ASP* 1.3 82.0 - - + +
346I LEU* 1.3 64.0 + - - +
347I THR* 3.9 9.4 + - - -
383I CYS* 4.9 3.1 - - - -
104K TYR 2.8 27.4 + - - -
105K HIS* 3.7 15.3 - + + -
107K LYS* 3.9 16.9 + - + +
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Residues in contact with LEU 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I TYR* 3.3 7.3 - - - +
304I VAL* 2.8 39.0 + - + +
342I LEU* 4.2 18.8 - - + -
344I ASP* 3.9 10.8 - - + +
345I TYR* 1.3 78.5 - - - +
347I THR* 1.3 61.1 + - - +
348I VAL* 3.8 14.7 + - + +
354I ILE* 4.1 28.5 - - + -
376I LEU* 4.1 23.3 - - + -
378I PHE* 4.4 17.9 - - + -
383I CYS* 4.0 7.2 - - - -
385I THR* 4.2 19.3 - - + +
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Residues in contact with THR 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I ASP 4.2 1.8 - - - -
303I TYR* 3.7 21.8 - - + -
345I TYR* 3.9 10.6 + - - -
346I LEU* 1.3 72.5 - - - +
348I VAL* 1.3 58.0 + - - +
352I GLU* 4.2 1.7 - - - +
378I PHE* 3.8 14.6 - - - -
382I LEU* 3.8 32.7 + - + +
383I CYS* 3.5 17.7 - - - +
105K HIS 5.2 0.3 + - - -
108K HIS* 4.2 17.7 + - + +
319K HIS* 3.5 32.5 - - + +
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Residues in contact with VAL 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I VAL* 4.2 3.8 - - + -
298I ILE* 3.7 36.1 - - + -
301I ASN* 3.4 0.2 - - - -
302I ASP 3.0 37.5 + - - +
303I TYR 4.6 0.2 - - - +
304I VAL* 4.1 16.8 - - + -
346I LEU* 3.8 25.8 - - + +
347I THR* 1.3 76.8 - - - +
349I ARG* 1.3 63.3 - - - +
352I GLU* 3.7 3.4 - - - -
354I ILE* 5.1 0.2 - - + -
378I PHE* 3.7 21.8 - - + -
319K HIS* 2.9 19.9 - - - -
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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