Contacts of the strand formed by residues 315 - 325 (chain M) in PDB entry 2X1W
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 315 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308M ALA* 4.2 16.6 - - + -
309M ALA 3.2 10.1 - - - +
310M SER* 2.8 25.1 + - - +
314M MET* 1.3 79.2 - - - +
316M LYS* 1.3 74.8 + - - +
317M LYS* 4.9 9.3 - - + +
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Residues in contact with LYS 316 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M ILE* 3.2 40.2 - - + +
224M TYR 3.4 18.8 + - - +
225M ASP* 4.4 3.4 - - - -
226M VAL* 3.5 22.7 - - + +
308M ALA* 3.6 0.3 - - - -
309M ALA 2.9 29.6 + - - -
314M MET* 3.5 19.3 - - + -
315M THR* 1.3 79.9 - - - +
317M LYS* 1.3 63.6 + - - +
1S NAG 4.5 15.1 + - - +
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Residues in contact with LYS 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226M VAL* 4.2 7.4 - - - +
261M GLU* 6.0 1.1 - - - +
306M THR* 4.2 17.6 - - + +
307M CYS 3.0 16.6 - - - +
308M ALA* 3.6 18.8 - - + -
315M THR* 4.9 8.1 - - + +
316M LYS* 1.3 77.9 - - - +
318M ASN* 1.3 67.3 + - - +
1S NAG 4.7 6.4 + - - +
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Residues in contact with ASN 318 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226M VAL* 2.6 29.5 + - + +
227M VAL* 3.9 2.9 - - - +
228M LEU* 3.9 17.5 - - + +
306M THR* 3.5 3.8 - - - +
307M CYS* 2.9 31.6 + - + +
317M LYS* 1.3 73.6 - - - +
319M SER* 1.3 67.9 + - - +
1S NAG 1.4 75.1 + - - +
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Residues in contact with SER 319 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228M LEU* 3.4 9.2 - - - +
231M SER 4.3 2.1 - - - +
304M LEU* 3.7 18.8 - - - +
305M TYR 3.1 15.3 - - - -
306M THR* 3.7 16.4 - - - -
318M ASN* 1.3 87.9 + - - +
320M THR* 1.3 65.9 + - - +
1S NAG 4.2 10.6 - - - +
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Residues in contact with THR 320 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228M LEU* 3.7 17.5 - - + -
230M PRO 4.3 1.3 - - - +
231M SER 2.9 30.4 + - - -
232M HIS* 3.5 9.7 + - - -
234M ILE* 4.1 21.9 - - + +
244M LEU* 4.2 17.0 - - + -
304M LEU* 3.7 6.2 - - - +
305M TYR* 3.0 27.2 + - + +
319M SER* 1.3 78.6 - - - +
321M PHE* 1.3 66.3 + - - +
322M VAL* 3.7 3.9 + - + -
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Residues in contact with PHE 321 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M GLY 4.9 2.9 + - - -
234M ILE* 4.0 13.9 + - - +
302M GLN* 4.0 15.5 - - + -
303M GLY* 3.4 35.2 - - - -
304M LEU* 3.8 15.0 - - + +
320M THR* 1.3 79.4 + - - +
322M VAL* 1.3 65.8 + - - +
323M ARG* 3.6 40.7 + - + +
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Residues in contact with VAL 322 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M ILE* 3.9 37.9 - - + -
236M LEU* 4.3 11.7 - - + -
242M LEU* 4.2 14.6 - - + -
244M LEU* 4.9 1.6 - - + -
301M ASP* 4.2 7.2 - - + +
302M GLN* 3.3 6.8 - - - +
303M GLY 2.9 31.4 + - - -
305M TYR* 3.7 31.4 - - + +
320M THR* 3.7 4.5 + - + -
321M PHE* 1.3 77.5 - - - +
323M ARG* 1.3 71.5 + - - +
324M VAL* 4.1 13.9 - - + -
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Residues in contact with ARG 323 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M ILE 3.1 15.8 + - - +
235M GLU* 3.4 27.4 + - + -
236M LEU 3.0 24.1 + - - -
302M GLN* 3.5 24.2 + - - +
321M PHE* 3.6 29.9 - - + +
322M VAL* 1.3 74.0 - - - +
324M VAL* 1.3 67.9 + - - +
325M HIS* 6.0 2.6 - - - +
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Residues in contact with VAL 324 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236M LEU* 3.4 13.2 - - + +
238M VAL* 4.1 14.8 - - + +
297M VAL* 3.7 28.3 - - + -
298M THR 3.8 21.5 - - - +
299M ARG* 4.3 11.4 - - - +
301M ASP* 4.0 4.3 - - + -
302M GLN* 2.9 47.0 + - + +
322M VAL* 4.1 9.4 - - + -
323M ARG* 1.3 81.4 + - - +
325M HIS* 1.3 64.5 + - - +
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Residues in contact with HIS 325 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M GLU* 3.8 31.4 + - + +
236M LEU* 3.1 27.6 + - - -
237M SER* 3.0 23.6 + - - -
238M VAL* 3.4 23.6 + - - +
299M ARG* 5.0 2.7 - - - +
323M ARG* 5.5 2.9 - - - +
324M VAL* 1.3 74.9 - - - +
326M GLU* 1.3 70.7 + - - +
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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