Contacts of the helix formed by residues 305 - 318 (chain A) in PDB entry 6YB9
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 GLY 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A THR* 3.9 1.0 + - - -
301A SER* 3.0 14.8 + - - +
304A LYS* 1.3 80.6 - - - +
306A PRO* 1.4 66.8 - - - +
307A ASP* 3.2 13.0 - - - -
308A GLU* 3.1 11.5 + - - +
309A THR* 3.0 22.7 + - - -
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Residues in contact with PRO 306 (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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301A SER 3.5 0.4 - - - -
302A ALA* 3.2 25.1 - - + +
303A HIS 4.1 5.4 - - - +
304A LYS 3.7 4.0 - - - -
305A GLY* 1.4 90.7 - - - +
307A ASP* 1.3 65.4 + - + +
309A THR* 3.3 10.3 + - - +
310A LEU* 3.2 31.6 + - + +
338A VAL* 5.5 9.1 - - + +
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Residues in contact with ASP 307 (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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305A GLY* 3.4 17.0 - - - -
306A PRO* 1.3 78.8 - - + +
308A GLU* 1.3 68.0 + - - +
310A LEU* 3.5 10.9 + - - +
311A ARG* 3.2 21.7 + - - +
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Residues in contact with GLU 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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298A ARG* 5.3 1.0 + - - -
299A VAL 5.6 1.3 - - - +
300A THR* 4.0 5.8 - - - +
305A GLY* 3.1 13.7 + - - +
307A ASP* 1.3 81.5 - - - +
309A THR* 1.3 60.9 + - - +
311A ARG* 2.8 43.5 + - - +
312A ILE* 2.9 50.3 + - + +
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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
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271A LEU* 5.3 1.1 - - + +
300A THR* 2.7 30.0 + - + +
301A SER 3.2 13.3 + - - -
302A ALA* 4.9 0.4 - - - -
305A GLY 3.0 11.9 + - - -
306A PRO* 3.3 12.1 + - - +
308A GLU* 1.3 75.7 - - - +
310A LEU* 1.3 60.3 + - + +
312A ILE* 3.4 2.9 + - - +
313A LYS* 3.0 27.8 + - - +
335A LEU* 3.7 26.0 - - + -
338A VAL* 4.5 14.6 - - + -
339A MET* 3.9 20.2 - - + +
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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
----------------------------------------------------------
306A PRO* 3.2 18.5 + - + +
307A ASP* 3.7 9.6 - - - +
309A THR* 1.3 76.9 - - + +
311A ARG* 1.3 58.2 + - - +
313A LYS* 3.5 30.7 + - + +
314A ALA* 3.0 27.5 + - - +
338A VAL* 4.7 13.7 - - + +
339A MET* 5.9 1.6 - - - -
342A ASN* 4.0 26.5 - - + +
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ARG* 4.7 4.6 - - - +
307A ASP 3.2 14.7 + - - +
308A GLU* 2.8 42.9 + - - +
310A LEU* 1.3 71.0 - - - +
312A ILE* 1.3 72.6 + - - +
314A ALA* 3.2 9.1 + - - +
315A GLU* 2.7 60.2 + - - +
122B TYR* 4.2 17.8 + - - +
123B PRO* 4.9 6.5 - - + -
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Residues in contact with ILE 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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271A LEU* 4.2 20.9 - - + -
298A ARG* 3.7 33.4 - - + +
299A VAL 4.2 8.5 - - - +
300A THR* 3.9 21.5 - - + -
308A GLU* 2.9 48.7 + - + +
309A THR* 3.8 4.3 - - - +
311A ARG* 1.3 74.9 - - - +
313A LYS* 1.3 68.5 + - - +
315A GLU* 3.1 17.7 + - - +
316A TYR* 3.3 32.6 - - + -
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Residues in contact with LYS 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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271A LEU* 6.0 0.8 - - - +
309A THR 3.0 17.5 + - - +
310A LEU* 3.5 35.4 + - + +
312A ILE* 1.3 75.7 - - - +
314A ALA* 1.3 60.1 + - - +
316A TYR* 3.1 6.9 + - - +
317A GLU* 2.7 60.4 + - + +
325A PHE* 4.0 11.5 - - + -
339A MET* 3.8 31.0 - - + +
342A ASN* 3.1 37.9 + - + +
343A THR* 4.0 5.6 - - - -
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Residues in contact with ALA 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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310A LEU 3.0 14.5 + - - +
311A ARG 3.4 9.6 - - - +
312A ILE 3.2 0.4 - - - -
313A LYS* 1.3 75.2 - - - +
315A GLU* 1.3 63.3 - - - +
317A GLU* 3.7 14.8 - - - +
318A GLY* 3.1 22.3 + - - -
102B ARG* 4.9 0.7 + - - -
122B TYR* 3.8 7.5 - - - +
123B PRO* 3.7 42.6 - - + +
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Residues in contact with GLU 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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298A ARG* 3.2 30.4 + - - -
311A ARG* 2.7 51.2 + - - +
312A ILE* 3.1 12.1 + - - +
314A ALA* 1.3 76.3 - - - +
316A TYR* 1.3 68.2 + - + +
318A GLY 3.8 4.9 + - - -
319A ASP* 4.0 16.5 + - - +
122B TYR* 4.0 33.2 - - + +
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Residues in contact with TYR 316 (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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267A ARG* 3.0 43.7 + - - +
269A VAL* 3.6 39.5 - - + -
296A GLU* 2.8 34.9 + - - +
298A ARG* 3.0 42.4 + - + +
312A ILE* 3.3 28.9 - - + -
313A LYS 3.1 5.6 + - - +
315A GLU* 1.3 79.7 - - + +
317A GLU* 1.3 64.9 + - - +
318A GLY 3.2 1.6 - - - -
319A ASP* 3.4 4.4 - - - +
321A ILE 4.1 1.9 + - - +
323A THR* 4.0 6.0 + - + -
325A PHE* 3.8 19.3 - + + -
345A TYR* 4.0 7.1 + - - -
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LYS* 2.7 49.3 + - + +
314A ALA* 3.5 12.2 + - - +
316A TYR* 1.3 78.1 - - - +
318A GLY* 1.3 52.3 + - - +
319A ASP 3.6 0.4 - - - -
325A PHE* 4.8 2.0 - - + -
342A ASN 3.5 0.7 - - - +
343A THR* 2.8 41.0 + - - +
344A ALA 4.3 1.4 + - - -
345A TYR* 4.0 21.9 + - + -
506A EDO 2.7 26.0 + - - -
102B ARG* 4.8 1.1 + - - -
174B GLU* 4.9 13.2 - - - +
178B LYS* 4.5 2.4 + - - -
399B TRP* 5.9 8.1 - - + -
403B ARG* 6.1 0.9 - - - -
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Residues in contact with GLY 318 (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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314A ALA 3.1 16.2 + - - -
315A GLU 3.8 0.4 + - - -
316A TYR 3.2 1.0 - - - -
317A GLU* 1.3 76.9 - - - +
319A ASP* 1.3 57.3 + - - +
506A EDO 3.5 9.9 - - - -
102B ARG* 3.5 43.3 + - - +
120B LYS* 5.7 1.4 + - - -
122B TYR* 3.6 13.5 + - - -
177B GLU* 4.7 0.3 - - - +
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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