Contacts of the helix formed by residues 307 - 317 (chain B) in PDB entry 4YCV
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 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B THR* 4.2 1.6 - - - -
304B ARG* 3.3 31.6 - - - +
306B ALA* 1.3 76.2 - - - +
308B GLU* 1.3 63.2 + - - +
309B LEU 3.6 1.8 - - - -
310B PRO* 3.3 15.6 - - - +
311B LEU* 3.2 22.7 - - - +
324B GLU* 3.8 24.8 - - + +
326B GLY 5.6 1.6 - - - +
328B VAL* 4.1 15.9 - - + -
344B SER* 4.6 4.5 - - - +
346B GLU* 3.1 34.7 + - + +
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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
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305B ILE* 5.8 3.3 - - - +
306B ALA* 3.4 23.5 - - + +
307B THR* 1.3 77.3 - - - +
309B LEU* 1.3 83.6 + - + +
311B LEU* 3.1 5.0 + - - +
312B LYS* 2.9 37.0 + - - +
346B GLU* 3.3 13.0 + - - +
348B TYR* 3.3 26.0 + - - +
478B LEU* 3.9 26.3 - - - +
505B TYR* 4.2 5.0 + - - -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASN* 5.8 5.2 - - - +
281B ILE* 4.9 17.0 - - + -
306B ALA 6.0 1.3 - - - +
308B GLU* 1.3 98.3 - - + +
310B PRO* 1.3 71.0 - - + +
312B LYS* 3.4 17.1 + - - +
313B MET* 3.0 28.7 + - - +
478B LEU* 5.4 5.2 - - + -
536B ASP* 5.4 14.6 - - + +
539B PHE* 4.4 32.4 - - + -
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Residues in contact with PRO 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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576A PHE* 3.8 27.9 - - + -
275B THR* 3.6 24.7 - - + -
276B PRO* 4.7 7.9 - - + +
279B ASN* 5.7 8.1 - - - +
306B ALA 5.4 1.6 - - - +
307B THR* 3.3 18.8 - - - +
309B LEU* 1.3 95.3 - - + +
311B LEU* 1.3 55.6 - - - +
313B MET* 3.2 14.8 + - + +
314B LEU* 2.9 31.7 + - - +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 3.5 31.9 - - + -
275B THR* 3.7 13.9 - - + -
307B THR* 3.2 35.7 - - - +
308B GLU 3.1 7.5 + - - +
310B PRO* 1.3 74.9 - - - +
312B LYS* 1.3 61.4 + - - +
314B LEU* 2.8 22.8 + - + +
315B ILE* 2.9 16.1 + - - +
322B VAL* 3.9 13.7 - - + +
323B TYR* 4.7 2.5 - - - -
324B GLU* 4.2 8.5 - - + +
346B GLU* 3.5 24.7 - - + +
347B PHE* 4.9 0.2 - - - -
348B TYR* 3.7 21.3 - - + -
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Residues in contact with LYS 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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308B GLU* 2.9 23.6 + - - +
309B LEU* 3.7 12.9 - - - +
311B LEU* 1.3 76.2 - - - +
313B MET* 1.3 56.2 + - - +
315B ILE* 3.0 13.8 + - - +
316B VAL* 3.0 29.9 + - - +
348B TYR* 3.5 31.7 + - + -
478B LEU* 3.7 14.3 - - - +
505B TYR* 3.6 12.1 + - - -
507B GLU* 3.0 45.3 + - + +
539B PHE* 3.4 38.1 - - + -
547B LEU* 3.4 8.5 - - + +
550B THR* 6.2 0.9 - - + -
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Residues in contact with MET 313 (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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235A ARG 4.4 12.3 - - - +
236A GLN* 5.0 0.2 - - - -
237A ARG 4.8 0.7 - - - +
238A TYR* 3.5 37.0 - - + +
576A PHE* 3.7 27.1 - - + -
309B LEU* 3.0 20.7 + - - +
310B PRO* 3.3 17.9 - - + +
311B LEU 3.1 0.2 - - - -
312B LYS* 1.3 75.8 - - - +
314B LEU* 1.3 59.0 + - - +
316B VAL* 3.3 13.2 - - - +
317B GLY 3.0 19.8 + - - -
538B ALA* 4.4 20.6 - - + +
539B PHE* 4.6 8.7 - - + -
542B SER* 3.2 22.0 - - - +
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Residues in contact with LEU 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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237A ARG* 4.9 1.6 - - + -
238A TYR 6.1 0.7 - - - +
241A LEU* 4.0 23.3 - - + -
575A LEU* 4.1 14.1 - - + -
576A PHE* 3.7 26.5 - - + -
273B VAL* 3.6 44.6 - - + -
275B THR* 5.3 1.3 - - + -
310B PRO 2.9 15.7 + - - +
311B LEU* 2.8 15.5 + - + +
313B MET* 1.3 73.2 - - - +
315B ILE* 1.3 60.8 + - - +
317B GLY* 2.9 16.3 + - - +
318B GLY 3.2 9.9 + - - -
319B ILE* 3.2 24.8 + - + +
322B VAL* 3.8 10.8 - - + -
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Residues in contact with ILE 315 (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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138A ARG* 4.6 1.0 + - - -
311B LEU 2.9 16.9 + - - +
312B LYS* 3.0 10.3 + - - +
314B LEU* 1.3 72.9 - - - +
316B VAL* 1.3 64.9 + - - +
318B GLY* 3.4 10.2 + - - -
319B ILE 3.1 24.2 - - - +
320B ASP* 3.2 25.6 - - - +
322B VAL* 3.9 6.1 - - + -
348B TYR* 3.4 35.9 - - + +
350B ALA* 4.3 4.9 - - + -
547B LEU* 3.5 9.6 - - + -
548B PRO* 3.7 20.3 - - + +
550B THR* 3.5 29.4 - - + +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 2.5 32.9 + - - +
238A TYR* 3.9 24.5 - - + -
242A LEU* 4.2 5.3 - - + +
312B LYS 3.0 14.9 + - - +
313B MET* 3.3 13.9 - - - +
315B ILE* 1.3 76.5 - - - +
317B GLY* 1.3 58.0 + - - +
318B GLY 3.2 3.2 + - - -
539B PHE* 6.1 0.4 - - + -
542B SER* 3.7 25.1 - - - +
543B LEU* 5.3 1.6 - - + -
545B TYR* 4.4 5.6 - - + -
546B GLY 3.2 19.1 - - - +
547B LEU* 3.5 26.9 - - + +
548B PRO* 4.7 0.7 - - - -
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 3.5 28.9 - - - -
241A LEU* 3.3 35.5 - - - +
242A LEU* 3.8 6.4 + - - +
248A ARG* 5.1 1.9 + - - -
313B MET 3.0 7.8 + - - -
314B LEU* 2.9 13.0 + - - -
316B VAL* 1.3 75.5 - - - +
318B GLY* 1.3 57.3 + - - +
319B ILE* 3.6 1.2 - - - +
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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