Contacts of the helix formed by residues 306 - 316 (chain I) in PDB entry 3SWD
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 MET 306 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232I ARG 5.3 0.7 - - - +
233I ILE* 3.6 30.5 - - + +
236I GLY* 3.4 30.7 - - - +
237I THR 3.7 3.4 - - - +
240I VAL* 3.8 10.5 - - + -
259I LEU* 5.7 1.3 - - + -
262I VAL* 4.1 11.9 - - + -
302I PHE* 3.8 15.5 - - + -
303I PRO* 3.0 26.2 + - + +
305I ASP* 1.3 77.8 - - - +
307I GLN* 1.3 63.9 + - - +
309I GLN* 3.3 43.7 + - + +
310I PHE* 3.1 33.4 + - + -
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Residues in contact with GLN 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I THR* 3.9 15.5 - - + -
302I PHE* 4.1 6.5 - - + -
303I PRO 3.6 2.6 + - - +
304I THR 2.9 14.2 + - - +
306I MET* 1.3 74.8 - - - +
308I ALA* 1.3 63.4 + - - +
310I PHE* 3.3 3.0 + - - -
311I THR* 2.8 36.0 + - - -
323I ILE* 3.5 25.7 - - + +
325I GLU* 2.9 29.8 + - + +
331I ARG* 3.0 30.9 + - - +
332I PHE* 3.8 16.4 - - + -
334I HIS* 3.0 30.0 + - - -
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Residues in contact with ALA 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304I THR 4.6 1.6 + - - -
307I GLN* 1.3 78.6 + - - +
309I GLN* 1.3 64.4 + - - +
311I THR* 3.3 3.5 + - - -
312I LEU* 3.1 17.3 + - - +
334I HIS* 3.5 28.4 - - + +
338I LEU* 5.1 0.7 - - - +
372I ALA* 3.4 47.4 - - + +
375I SER* 3.5 15.4 + - - +
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Residues in contact with GLN 309 (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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233I ILE* 4.2 0.6 - - - +
237I THR* 3.1 36.5 + - + +
240I VAL* 3.8 22.1 - - + +
305I ASP 3.1 27.3 + - - +
306I MET* 3.3 33.0 - - + +
307I GLN 3.2 0.4 - - - -
308I ALA* 1.3 84.2 + - - +
310I PHE* 1.3 63.1 + - - +
312I LEU* 3.2 7.4 + - - +
313I LEU* 3.1 15.6 + - - +
371I ARG 4.3 7.6 + - - -
372I ALA* 4.6 2.7 - - - -
374I ALA* 5.3 0.2 - - + -
375I SER* 4.3 16.4 - - - +
378I LEU* 4.8 4.7 - - + -
399I TYR* 3.6 12.5 + - - -
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Residues in contact with PHE 310 (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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240I VAL* 3.7 19.1 - - + -
262I VAL* 4.0 16.2 - - + -
265I LYS* 3.6 24.2 - - + -
266I LEU* 3.6 35.2 - - + -
269I ALA* 5.8 0.2 - - + -
292I VAL* 4.3 19.3 - - + -
294I VAL* 4.5 3.6 - - + -
302I PHE* 3.3 37.9 - + + -
306I MET* 3.1 26.4 + - + +
307I GLN 3.3 0.9 + - - +
309I GLN* 1.3 73.7 - - - +
311I THR* 1.3 59.4 + - - +
313I LEU* 3.2 15.5 + - + +
314I ASN* 3.0 28.6 + - - +
323I ILE* 3.5 18.4 - - + +
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Residues in contact with THR 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307I GLN* 2.8 33.4 + - - -
308I ALA 3.4 8.5 - - - -
309I GLN 3.2 0.2 - - - -
310I PHE* 1.3 76.2 - - - +
312I LEU* 1.3 58.0 + - - +
314I ASN* 3.4 3.9 + - - +
315I LEU* 3.0 50.5 + - + +
323I ILE* 3.3 15.1 - - - +
334I HIS* 4.0 15.9 - - + +
335I VAL* 4.3 14.6 - - + -
338I LEU* 4.8 1.1 - - + -
352I VAL* 4.4 10.1 - - + +
354I CYS* 4.1 13.9 - - - -
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Residues in contact with LEU 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I VAL* 5.5 0.4 - - + -
244I ILE* 3.7 18.8 - - + -
308I ALA 3.1 12.5 + - - +
309I GLN 3.6 9.2 - - - +
311I THR* 1.3 74.3 - - - +
313I LEU* 1.3 66.7 + - - +
315I LEU* 3.0 16.5 + - + +
316I VAL* 3.3 16.0 + - + +
338I LEU* 4.3 18.6 - - + +
360I LEU* 3.9 27.6 - - + -
375I SER* 3.4 28.7 - - - +
378I LEU* 3.7 17.9 - - + -
379I ALA* 3.6 20.9 - - + +
382I ILE* 4.8 2.2 - - + -
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Residues in contact with LEU 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I VAL* 4.7 5.8 - - + -
243I ALA* 4.1 17.7 - - + -
244I ILE* 3.8 19.7 - - + +
266I LEU* 4.1 26.5 - - + -
269I ALA* 4.1 24.9 - - + -
289I PRO* 4.2 14.5 - - + +
290I LYS 4.3 7.2 - - - +
292I VAL* 4.5 9.0 - - + -
309I GLN 3.1 12.4 + - - +
310I PHE* 3.2 18.3 + - + +
312I LEU* 1.3 79.0 - - - +
314I ASN* 1.3 76.8 + - - +
316I VAL* 3.2 4.9 + - - +
317I ALA* 3.1 22.8 + - + +
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Residues in contact with ASN 314 (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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291I ALA* 3.4 8.2 - - - +
292I VAL* 2.9 54.0 + - - +
310I PHE 3.0 13.9 + - - +
311I THR 3.8 2.9 - - - +
313I LEU* 1.3 78.5 - - - +
315I LEU* 1.3 62.5 + - - +
317I ALA* 3.1 16.0 + - - +
319I GLY 4.8 1.6 - - - +
321I GLY* 3.9 16.2 + - - +
323I ILE* 3.9 24.5 - - - +
354I CYS* 3.7 21.7 - - + +
356I GLY* 3.5 14.4 + - - -
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Residues in contact with LEU 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311I THR* 3.0 34.5 + - + +
312I LEU* 3.0 11.1 + - + +
314I ASN* 1.3 76.3 - - - +
316I VAL* 1.3 60.5 + - + +
317I ALA 3.5 0.2 - - - -
335I VAL* 5.6 3.1 - - + +
338I LEU* 3.6 31.4 - - + -
343I ALA* 3.9 27.1 - - + +
344I HIS 3.5 26.7 - - - +
345I ALA* 3.8 14.1 - - + -
354I CYS* 3.7 19.1 - - + -
355I HIS 4.2 3.1 - - - +
356I GLY* 3.4 3.0 - - - -
357I VAL* 3.0 29.8 + - - +
360I LEU* 4.9 1.6 - - + +
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Residues in contact with VAL 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I ILE* 4.2 28.3 - - + +
288I ARG* 3.2 22.3 + - - +
289I PRO* 4.2 7.6 - - + +
312I LEU* 3.6 11.0 - - + +
313I LEU 3.5 10.3 - - - +
315I LEU* 1.3 80.9 - - - +
317I ALA* 1.3 60.2 + - - +
357I VAL* 3.3 16.0 - - + +
358I GLU 5.0 6.1 - - - +
359I LYS* 5.5 0.4 - - - -
360I LEU* 3.9 37.0 - - + +
382I ILE* 4.1 14.8 - - + -
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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