Contacts of the strand formed by residues 307 - 318 (chain x) in PDB entry 5GJQ
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 ASN 307 (chain x).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298x THR* 3.2 28.8 - - + +
299x LYS 3.1 10.5 - - - +
300x GLN* 3.3 33.9 + - - +
306x ARG* 1.3 78.3 - - - +
308x ALA* 1.3 58.3 + - - +
2y GLN* 3.6 13.3 + - - -
14y THR* 5.0 1.9 + - - -
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Residues in contact with ALA 308 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256x CYS* 4.6 1.8 - - - -
258x GLU* 3.9 23.1 - - - +
298x THR* 3.2 22.4 - - - -
299x LYS 2.8 11.3 + - - +
301x SER* 4.4 5.2 - - - -
304x LEU* 4.5 6.1 - - + -
306x ARG* 3.1 14.1 + - + +
307x ASN* 1.3 74.4 - - - +
309x LEU* 1.3 61.8 + - - +
310x TYR* 3.0 26.9 + - + -
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Residues in contact with LEU 309 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256x CYS* 4.7 0.4 - - - -
257x THR* 2.4 67.7 + - + +
258x GLU* 4.0 10.2 + - - +
296x GLU* 4.0 34.3 - - + +
297x ILE 4.0 1.8 - - - +
298x THR* 4.8 9.6 - - - +
308x ALA* 1.3 73.7 - - - +
310x TYR* 1.3 59.1 + - - +
311x ILE* 5.4 1.3 - - + -
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Residues in contact with TYR 310 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254x MET* 4.1 19.5 - - + -
255x LYS 3.7 3.8 - - - -
256x CYS* 3.8 24.5 - - + +
262x GLU* 3.1 24.0 + - + +
265x THR* 6.1 0.2 - - - -
296x GLU* 3.8 2.3 - - - -
297x ILE* 2.8 41.7 + - + +
299x LYS* 3.3 48.0 - - + -
300x GLN 5.3 0.2 - - - -
301x SER* 2.7 43.7 + - - -
302x PRO* 4.5 3.8 - - - +
308x ALA* 3.0 13.9 + - + -
309x LEU* 1.3 78.0 - - - +
311x ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 311 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253x THR 3.9 0.5 - - - +
254x MET* 3.1 8.3 - - - +
255x LYS* 2.7 50.0 + - + +
256x CYS 5.6 0.4 - - - -
257x THR* 3.4 32.1 - - + +
294x GLN* 4.0 16.8 - - + +
295x GLU 3.6 13.5 - - - +
296x GLU* 5.1 9.4 - - + -
297x ILE* 4.8 0.9 - - - +
309x LEU* 5.4 1.3 - - + -
310x TYR* 1.3 79.4 - - - +
312x LYS* 1.3 73.3 + - - +
313x SER* 6.2 0.2 - - - -
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Residues in contact with LYS 312 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252x THR* 4.7 9.2 - - - +
253x THR 3.6 4.9 - - - +
254x MET* 4.4 6.1 - - + -
269x GLU* 4.1 21.1 + - - -
293x LEU 3.7 12.6 - - - +
294x GLN* 3.3 25.3 - - - +
295x GLU* 2.9 48.1 + - + +
297x ILE* 3.6 30.2 - - + +
311x ILE* 1.3 81.1 - - - +
313x SER* 1.3 59.7 + - - +
314x SER* 3.7 15.2 + - - +
6y LYS* 4.9 2.2 - - - +
12y THR* 5.1 2.9 + - - +
66y THR* 4.6 15.0 + - - +
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Residues in contact with SER 313 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251x GLU 3.3 1.9 - - - +
252x THR* 3.1 7.2 - - - -
253x THR* 2.8 59.0 + - - +
293x LEU 4.5 0.4 - - - -
294x GLN* 4.8 14.6 + - - +
311x ILE* 6.2 0.4 - - - -
312x LYS* 1.3 72.2 - - - +
314x SER* 1.3 62.0 + - - +
315x LYS* 4.3 10.8 - - - +
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Residues in contact with SER 314 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250x PHE* 4.1 26.0 - - - -
251x GLU 3.3 4.5 - - - -
252x THR* 4.2 10.1 - - - -
269x GLU* 5.5 1.6 + - - -
292x ARG 5.5 0.4 - - - -
293x LEU* 3.5 43.0 + - - +
294x GLN* 5.5 0.6 - - - +
312x LYS* 3.7 22.9 + - - +
313x SER* 1.3 74.7 + - - +
315x LYS* 1.3 67.5 + - - +
357x LEU 5.0 0.3 - - - +
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Residues in contact with LYS 315 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250x PHE* 3.9 5.3 - - - -
251x GLU* 3.0 29.3 + - + +
293x LEU* 5.3 0.9 - - - -
313x SER* 5.3 9.9 - - - +
314x SER* 1.3 80.1 - - - +
316x ILE* 1.3 60.1 + - - +
317x SER 2.9 10.0 + - - -
356x GLU 5.3 3.6 + - - -
357x LEU* 3.9 12.7 - - - +
358x CYS 2.9 29.2 + - - +
359x THR* 4.1 6.7 - - + +
360x PRO* 4.3 20.0 - - + -
363x GLN* 5.6 2.5 - - - +
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Residues in contact with ILE 316 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248x VAL* 4.7 1.8 - - + -
249x GLU 3.9 7.2 - - - +
250x PHE* 3.7 23.1 - - + -
274x LEU* 4.3 13.2 - - + -
293x LEU* 5.8 1.8 - - + -
315x LYS* 1.3 69.1 - - - +
317x SER* 1.3 63.1 + - - +
318x ARG 3.3 13.2 - - - +
319x LEU* 3.0 37.9 - - + -
354x MET* 3.4 33.9 - - + -
357x LEU* 3.2 25.7 + - + +
358x CYS* 3.3 13.3 - - + +
359x THR* 3.6 3.9 + - - -
362x LEU* 2.8 20.9 - - + +
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Residues in contact with SER 317 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249x GLU* 2.9 37.1 + - - +
250x PHE 3.3 15.3 - - - -
251x GLU* 3.9 4.2 + - - +
268x LYS* 3.8 20.8 + - - +
315x LYS 2.9 7.4 + - - -
316x ILE* 1.3 70.0 - - - +
318x ARG* 1.3 68.9 + - - +
359x THR* 3.7 11.5 + - - -
362x LEU* 2.9 19.9 - - - +
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Residues in contact with ARG 318 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238x LYS* 4.9 4.8 - - - +
247x GLY 5.3 0.4 - - - -
248x VAL* 3.6 5.9 - - - -
249x GLU* 3.4 44.7 + - + +
316x ILE* 3.2 11.5 + - - +
317x SER* 1.3 92.2 - - - +
319x LEU* 1.3 66.4 + - - +
362x LEU* 3.6 9.0 - - + -
365x LYS* 3.9 30.9 - - + +
409x ILE* 4.2 26.5 + - - +
410x GLY* 4.2 14.8 - - - +
412x ASN* 4.3 15.3 - - - +
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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