Contacts of the helix formed by residues 305 - 318 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B THR* 3.9 1.2 + - - -
301B SER* 2.9 15.3 + - - +
304B LYS* 1.3 80.4 - - - +
306B PRO* 1.4 66.6 - - - +
307B ASP* 3.3 13.0 - - - -
308B GLU* 3.1 11.7 + - - +
309B THR* 3.0 21.8 + - - -
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Residues in contact with PRO 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B SER 3.6 0.2 - - - -
302B ALA* 3.2 24.2 - - + +
303B HIS 4.1 5.4 - - - +
304B LYS 3.6 4.9 - - - +
305B GLY* 1.4 90.5 - - - +
307B ASP* 1.3 65.8 + - - +
309B THR* 3.3 10.5 + - - +
310B LEU* 3.2 31.8 + - + +
338B VAL* 5.5 8.7 - - + +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLY* 3.4 16.8 - - - -
306B PRO* 1.3 79.3 - - + +
308B GLU* 1.3 66.4 + - - +
310B LEU* 3.5 11.0 + - - +
311B ARG* 3.2 21.4 + - - +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 5.2 0.9 + - - -
299B VAL 5.7 1.3 - - - +
300B THR* 4.0 6.3 - - - +
305B GLY* 3.1 14.4 + - - +
307B ASP* 1.3 83.3 - - - +
309B THR* 1.3 65.1 + - - +
311B ARG* 2.8 44.4 + - - -
312B ILE* 2.9 46.0 + - + +
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU* 5.3 1.1 - - + +
300B THR* 2.6 29.8 + - + +
301B SER 3.3 13.2 + - - -
302B ALA* 3.9 2.2 + - - -
305B GLY 3.0 11.8 + - - -
306B PRO* 3.3 11.8 + - - +
308B GLU* 1.3 75.8 - - - +
310B LEU* 1.3 57.6 + - + +
312B ILE* 3.3 2.9 + - - +
313B LYS* 3.0 27.8 + - - +
335B LEU* 3.7 26.7 - - + -
338B VAL* 4.8 13.0 - - + -
339B MET* 3.9 19.9 - - + +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 6.5 0.2 - - - -
306B PRO* 3.2 18.9 + - + +
307B ASP* 3.7 10.5 - - - +
308B GLU 3.3 0.2 - - - -
309B THR* 1.3 74.7 - - + +
311B ARG* 1.3 59.0 + - - +
313B LYS* 3.4 30.4 - - + +
314B ALA* 3.0 26.9 + - - +
338B VAL* 4.4 14.8 - - + -
339B MET* 5.8 1.1 - - - -
342B ASN* 4.0 27.6 - - + +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 4.1 18.8 + - - +
123A PRO* 4.8 7.4 - - + -
298B ARG* 4.6 4.6 - - - +
307B ASP 3.2 12.5 + - - +
308B GLU* 2.8 43.8 + - - +
310B LEU* 1.3 73.8 - - - +
312B ILE* 1.3 73.4 + - - +
314B ALA* 3.2 9.3 + - - +
315B GLU* 2.7 59.5 + - - +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU* 4.1 21.1 - - + -
298B ARG* 3.7 32.1 - - + +
299B VAL 4.2 9.0 - - - +
300B THR* 3.8 26.0 - - + -
308B GLU* 2.9 43.5 + - + +
309B THR* 3.7 4.3 - - - +
311B ARG* 1.3 74.2 - - - +
313B LYS* 1.3 69.1 + - - +
315B GLU* 3.1 17.8 + - - +
316B TYR* 3.3 38.7 - - + -
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Residues in contact with LYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 6.4 0.2 - - - +
271B LEU* 6.0 0.8 - - - +
309B THR 3.0 14.1 + - - +
310B LEU* 3.4 29.0 + - + +
312B ILE* 1.3 75.8 - - - +
314B ALA* 1.3 57.7 + - - +
316B TYR* 3.1 7.1 + - - +
317B GLU* 2.8 60.1 + - + +
325B PHE* 4.0 11.2 - - + -
339B MET* 3.8 32.1 - - + +
342B ASN* 3.1 45.9 + - + +
343B THR* 4.1 5.2 - - - -
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ARG* 4.9 0.7 + - - -
122A TYR* 3.9 7.2 - - - +
123A PRO* 3.6 43.2 - - + +
310B LEU 3.0 14.7 + - - +
311B ARG* 3.4 9.9 - - - +
312B ILE 3.2 0.2 - - - -
313B LYS* 1.3 74.1 - - - +
315B GLU* 1.3 63.9 + - - +
317B GLU* 3.7 14.8 - - - +
318B GLY* 3.1 23.0 + - - -
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.9 32.5 - - + +
298B ARG* 3.0 32.6 + - - -
311B ARG* 2.7 49.0 + - - +
312B ILE* 3.1 11.5 + - - +
314B ALA* 1.3 75.9 - - - +
316B TYR* 1.3 67.6 + - + +
318B GLY 3.8 5.5 + - - -
319B ASP* 4.0 17.5 + - - +
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Residues in contact with TYR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ARG* 3.0 45.2 + - - +
269B VAL* 3.6 40.8 - - + -
296B GLU* 2.8 35.3 + - - +
298B ARG* 3.0 42.2 + - + +
312B ILE* 3.3 28.9 + - + -
313B LYS 3.1 6.0 + - - +
315B GLU* 1.3 78.4 - - + +
317B GLU* 1.3 64.4 + - - +
318B GLY 3.2 1.8 - - - -
319B ASP* 3.5 4.1 - - - +
321B ILE 4.1 1.9 + - - +
323B THR* 3.9 6.5 + - + -
325B PHE* 3.9 18.2 - + + -
345B TYR* 4.0 7.2 - - - -
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 4.8 0.9 + - - -
174A GLU* 5.1 9.5 - - - +
178A LYS* 4.6 1.7 + - - -
399A TRP* 6.0 7.7 - - + -
403A ARG* 6.2 0.2 - - - -
313B LYS* 2.8 51.5 + - + +
314B ALA* 3.7 12.8 - - - +
316B TYR* 1.3 77.8 - - - +
318B GLY* 1.3 52.3 + - - +
319B ASP 3.6 0.7 - - - -
320B GLY 5.0 0.2 - - - -
325B PHE* 4.8 1.8 - - + -
342B ASN 3.4 1.0 - - - +
343B THR* 2.8 40.1 + - - +
344B ALA 4.4 1.0 + - - -
345B TYR* 4.0 22.8 + - + -
701B EDO 2.6 26.3 + - - -
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Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 3.5 42.7 + - - +
120A LYS* 5.5 2.1 - - - -
122A TYR* 3.5 14.1 + - - -
314B ALA 3.1 16.8 + - - -
315B GLU 3.8 0.4 + - - -
316B TYR 3.2 1.0 - - - -
317B GLU* 1.3 76.4 - - - +
319B ASP* 1.3 58.6 + - - +
320B GLY 3.5 2.0 - - - -
701B EDO 3.5 9.0 - - - -
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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