Contacts of the strand formed by residues 307 - 315 (chain A) in PDB entry 4FQP
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A MET* 3.8 7.4 - - - +
306A ILE* 1.3 84.8 - - - +
308A THR* 1.3 73.0 + - - +
326A THR* 6.6 0.2 - - - -
327A VAL 3.7 6.3 - - - +
328A GLN* 3.5 21.3 - - + +
329A VAL 5.1 0.2 + - - -
1G NAG 1.4 63.7 + - - +
4G FUC 5.8 3.3 - - - -
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A THR* 3.7 10.3 - - - +
282A THR* 5.1 0.7 - - - -
283A MET* 2.7 36.6 - - + -
287A PRO* 3.4 25.3 - - + +
289A PHE* 4.0 19.4 - - - -
306A ILE* 4.3 6.7 - - + -
307A ASN* 1.3 79.6 - - - +
309A THR* 1.3 61.9 + - - +
310A LEU* 4.4 8.7 - - - +
326A THR* 4.5 1.1 - - - -
327A VAL* 3.1 43.2 + - - +
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Residues in contact with THR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR* 3.1 5.2 + - - -
282A THR* 2.9 51.0 + - - +
308A THR* 1.3 72.3 - - - +
310A LEU* 1.3 62.0 + - - +
324A GLU* 3.4 36.6 - - + +
325A LEU 3.4 9.0 - - - -
326A THR* 2.9 33.5 - - + +
4G FUC 5.7 0.7 - - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE* 4.1 8.5 - - + +
264A LEU* 4.4 15.7 - - + -
279A TRP* 4.6 10.8 - - + -
280A SER 3.8 5.6 - - - +
281A THR* 4.5 6.7 - - - -
286A LEU* 4.0 17.9 - - + -
287A PRO* 4.9 4.5 - - + -
289A PHE* 6.2 1.3 - - + -
290A ALA* 5.2 2.5 - - + -
297A LEU* 3.6 32.8 - - + -
299A ILE* 4.9 5.4 - - + -
308A THR* 4.4 12.8 - - - +
309A THR* 1.3 77.2 - - - +
311A ILE* 1.3 61.4 + - - +
323A ALA 3.3 6.8 - - - +
324A GLU* 3.3 3.6 - - - +
325A LEU* 2.8 37.1 + - + +
327A VAL* 3.8 26.0 - - + -
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ASN 3.6 2.6 - - - +
279A TRP* 3.7 6.0 - - - -
280A SER* 2.6 52.4 + - - +
281A THR 3.7 20.4 - - - +
282A THR* 3.8 14.8 - - - +
310A LEU* 1.3 77.6 - - - +
312A CYS* 1.3 64.4 + - - +
313A ASN* 4.3 5.8 - - + +
322A GLN* 3.9 32.1 - - + +
323A ALA 3.4 4.0 - - - +
324A GLU* 3.6 23.1 - - - +
420A NAG 5.8 0.9 - - - +
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Residues in contact with CYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL* 4.1 6.0 - - + +
248A ILE* 4.4 9.1 - - + +
266A CYS* 2.0 50.0 - - - -
277A TYR* 4.2 7.0 - - - -
278A ASN 3.6 7.0 - - - -
279A TRP* 4.0 24.3 - - + -
310A LEU 4.2 1.0 - - - -
311A ILE* 1.3 69.9 - - - +
313A ASN* 1.3 60.7 + - - +
314A VAL* 3.6 12.9 + - - -
322A GLN* 3.0 25.5 - - - -
323A ALA 3.2 10.4 + - - +
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLY 4.7 0.2 - - - -
277A TYR 3.7 0.7 - - - -
278A ASN* 2.8 59.2 + - + +
280A SER* 6.0 0.2 - - - +
311A ILE* 3.8 8.2 + - + -
312A CYS* 1.3 70.6 - - - +
314A VAL* 1.3 59.6 + - - +
315A THR* 3.9 1.6 + - - -
320A ALA* 3.9 7.8 - - - +
321A ARG 3.2 15.5 - - - +
322A GLN* 3.8 16.5 + - + -
420A NAG 1.5 68.0 + - - +
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PRO* 3.7 18.5 - - + +
246A VAL* 3.7 31.0 - - + -
266A CYS* 3.8 4.0 - - - -
268A ALA* 4.2 5.4 - - + -
274A PRO* 3.7 28.7 - - + -
276A GLY 3.4 7.0 - - - +
277A TYR* 3.8 16.4 - - + -
312A CYS* 3.6 27.4 - - - -
313A ASN* 1.3 70.8 - - - +
315A THR* 1.3 62.0 + - - +
320A ALA* 3.1 4.2 - - - -
321A ARG 2.8 34.6 + - - -
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A PRO* 3.7 1.7 - - - +
275A THR* 2.8 20.7 + - - +
276A GLY* 2.7 47.7 + - - +
313A ASN* 3.9 2.0 + - - -
314A VAL* 1.3 72.7 - - - +
316A ASN* 1.3 68.6 + - - +
319A GLY 3.6 5.2 - - - +
320A ALA* 3.4 17.2 - - - +
420A NAG 3.7 25.0 + - - -
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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