Contacts of the strand formed by residues 315 - 325 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308N ALA* 4.2 15.3 - - + -
309N ALA 3.2 12.1 - - - +
310N SER* 2.8 24.8 + - - +
314N MET* 1.3 80.3 + - - +
316N LYS* 1.3 74.5 + - - +
317N LYS* 4.9 8.8 - - + +
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Residues in contact with LYS 316 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223N ILE* 3.2 39.8 - - + +
224N TYR 3.5 18.1 + - - +
225N ASP* 4.4 3.4 - - - -
226N VAL* 3.4 20.2 - - + +
308N ALA* 3.6 0.3 - - - -
309N ALA 2.9 29.2 + - - -
314N MET* 3.5 20.2 - - + -
315N THR* 1.3 79.4 - - - +
317N LYS* 1.3 63.9 + - - +
1T NAG 4.1 24.4 + - + +
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Residues in contact with LYS 317 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226N VAL* 4.2 5.2 - - - -
261N GLU* 6.0 1.3 - - - +
306N THR* 4.2 17.6 - - + +
307N CYS 3.0 18.8 - - - +
308N ALA* 3.6 18.6 - - + -
315N THR* 4.9 8.1 - - + +
316N LYS* 1.3 76.0 - - - +
318N ASN* 1.3 59.7 + - - +
1T NAG 3.3 24.5 + - - +
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Residues in contact with ASN 318 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226N VAL* 2.6 25.1 + - + +
227N VAL* 4.0 2.3 - - - +
228N LEU* 3.8 19.2 - - + +
306N THR* 3.5 4.0 - - - +
307N CYS* 2.9 31.4 + - - +
317N LYS* 1.3 72.5 - - - +
319N SER* 1.3 75.7 + - - +
1T NAG 1.4 61.5 + - - +
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Residues in contact with SER 319 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228N LEU* 3.4 8.0 - - - +
231N SER 4.3 4.3 - - - +
304N LEU* 3.7 19.0 - - - +
305N TYR 3.1 16.2 - - - -
306N THR* 3.7 15.9 - - - -
318N ASN* 1.3 88.7 + - - +
320N THR* 1.3 65.9 + - - +
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Residues in contact with THR 320 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228N LEU* 3.7 17.7 - - + -
230N PRO 4.3 1.1 - - - +
231N SER 2.8 29.9 + - - -
232N HIS* 3.5 9.2 + - - -
234N ILE* 4.1 22.3 - - + +
244N LEU* 4.2 17.5 - - + -
304N LEU* 3.8 6.5 - - - +
305N TYR* 3.1 24.6 + - + +
319N SER* 1.3 78.8 - - - +
321N PHE* 1.3 64.3 + - - +
322N VAL* 3.7 4.3 + - + -
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Residues in contact with PHE 321 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233N GLY 4.8 2.9 + - - -
234N ILE* 4.0 13.7 + - - +
302N GLN* 4.0 15.5 - - + -
303N GLY* 3.4 34.8 - - - -
304N LEU* 3.8 14.7 - - + +
320N THR* 1.3 80.3 + - - +
322N VAL* 1.3 64.2 + - - +
323N ARG* 3.6 40.2 + - + +
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Residues in contact with VAL 322 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N ILE* 3.8 37.2 - - + -
236N LEU* 4.3 11.9 - - + -
242N LEU* 4.3 14.8 - - + -
244N LEU* 4.9 2.0 - - + -
301N ASP* 4.3 7.0 - - + +
302N GLN* 3.3 6.8 - - - +
303N GLY 2.9 31.9 + - - -
305N TYR* 3.7 30.5 - - + -
320N THR* 3.7 4.9 + - + +
321N PHE* 1.3 75.4 - - - +
323N ARG* 1.3 72.0 + - - +
324N VAL* 4.2 13.5 - - + -
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Residues in contact with ARG 323 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N ILE 3.0 15.3 + - - +
235N GLU* 3.4 27.7 + - + +
236N LEU 3.0 24.4 + - - -
302N GLN* 3.4 24.0 + - - +
321N PHE* 3.6 29.5 - - + +
322N VAL* 1.3 76.0 - - - +
324N VAL* 1.3 63.8 + - - +
325N HIS* 5.1 8.5 - - + +
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Residues in contact with VAL 324 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N LEU* 3.4 12.6 - - + +
238N VAL* 4.1 15.3 - - + +
297N VAL* 3.8 28.5 - - + -
298N THR 3.8 22.7 - - - +
299N ARG* 3.6 17.9 + - - +
301N ASP* 4.0 4.9 - - + -
302N GLN* 2.9 46.7 + - + +
322N VAL* 4.2 9.4 - - + -
323N ARG* 1.3 79.0 + - - +
325N HIS* 1.3 70.1 + - - +
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Residues in contact with HIS 325 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235N GLU* 3.1 43.4 + - + +
236N LEU 3.1 13.1 + - - -
237N SER* 3.4 18.5 + - - -
238N VAL* 3.0 30.0 + - - -
299N ARG* 3.9 9.9 - - - +
323N ARG* 4.9 10.1 - - + +
324N VAL* 1.3 79.6 - - - +
326N GLU* 1.3 71.5 + - - +
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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