Contacts of the strand formed by residues 306 - 313 (chain B) in PDB entry 6AHU
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 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B VAL* 3.5 5.3 - - - +
294B LEU* 2.7 41.8 + - - +
304B MET* 5.1 1.2 - - - +
305B LEU* 1.3 75.7 - - - +
307B PRO* 1.3 72.4 - - - +
308B VAL* 3.6 3.1 + - - +
335B LEU* 4.5 18.1 - - - +
339B ILE* 5.5 3.4 - - - -
663B PHE* 4.9 0.4 - - - -
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Residues in contact with PRO 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU 3.4 7.6 - - - +
293B VAL* 3.9 19.3 - - + -
306B GLY* 1.3 83.1 - - - +
308B VAL* 1.3 65.0 + - - +
309B THR* 6.1 0.2 - - - -
330B TRP 4.1 3.5 - - - +
331B LEU* 4.8 5.4 - - - -
332B HIS* 5.4 0.9 + - - +
335B LEU* 5.5 3.6 - - + -
659B VAL* 4.0 29.6 - - + +
663B PHE* 3.6 27.6 - - + -
807B ARG* 4.9 3.6 - - - +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B SER* 5.2 0.2 - - - -
292B LEU* 2.6 38.7 + - + +
294B LEU* 3.7 35.4 - - + -
306B GLY 3.6 3.8 + - - +
307B PRO* 1.3 78.8 - - - +
309B THR* 1.3 70.1 + - - +
310B PHE* 3.4 9.5 + - + +
329B ILE* 3.8 25.8 - - + -
330B TRP 3.3 33.4 - - - +
331B LEU* 4.5 7.2 - - + -
339B ILE* 5.4 3.1 - - + -
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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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289B GLN* 4.7 11.2 - - - +
290B GLY 3.3 9.4 - - - -
291B SER* 4.1 14.6 - - - +
307B PRO 4.4 0.4 - - - -
308B VAL* 1.3 74.0 - - - +
310B PHE* 1.3 59.9 + - - +
311B ILE* 4.2 3.1 + - - +
328B TRP 4.4 1.0 - - - +
330B TRP* 3.2 51.6 + - - +
431B ARG* 4.6 3.0 + - - +
433B ARG* 6.2 0.7 - - - +
602B GLN* 4.7 15.5 - - - +
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Residues in contact with PHE 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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266B LEU* 5.8 1.1 - - + -
278B PHE* 3.5 31.6 - + + -
289B GLN* 3.3 3.8 - - - +
290B GLY* 2.6 48.0 + - - +
292B LEU* 4.8 14.4 - - + -
294B LEU* 6.2 2.2 - - + -
308B VAL* 3.4 12.0 + - + +
309B THR* 1.3 73.2 - - - +
311B ILE* 1.3 74.0 + - - +
312B TRP* 3.2 42.0 - + - -
327B LEU* 3.6 37.5 - - + -
328B TRP 3.6 15.9 - - - -
329B ILE* 3.6 28.0 - - + -
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Residues in contact with ILE 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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289B GLN* 3.6 26.7 - - + +
309B THR 4.6 2.5 - - - +
310B PHE* 1.3 94.2 - - - +
312B TRP* 1.3 70.5 + - - +
313B LYS* 4.4 0.4 + - + -
326B GLN 4.6 0.2 - - - +
327B LEU* 3.8 19.9 - - - +
328B TRP* 4.0 19.8 + - + +
330B TRP* 3.6 41.3 - - + -
504B ILE* 3.8 16.2 - - + -
554B TRP* 4.0 26.1 - - + -
598B LEU* 5.5 2.5 - - + -
600B ILE* 3.8 11.7 - - + -
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Residues in contact with TRP 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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259B GLU* 6.0 0.4 - - + -
262B ILE* 3.6 21.3 - - + -
263B LEU* 3.7 17.5 - - + -
278B PHE* 2.5 53.9 + + + +
279B ALA 4.4 2.9 - - - -
281B VAL* 5.7 0.4 - - + -
284B LEU* 3.3 34.0 + - + +
285B SER* 3.0 23.3 - - - +
286B GLY* 5.1 1.6 - - - +
288B ARG 4.4 5.9 + - - +
289B GLN* 5.1 0.2 - - - +
310B PHE* 3.2 27.6 + + - -
311B ILE* 1.3 81.9 - - - +
313B LYS* 1.3 68.0 + - - +
325B ARG* 3.6 43.3 - - + -
326B GLN 4.7 3.4 - - - -
327B LEU* 3.8 18.2 - - + -
504B ILE* 4.5 4.9 - - - +
554B TRP* 4.7 0.4 - - - -
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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
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285B SER 3.4 7.6 - - - +
286B GLY* 5.4 4.9 - - - +
311B ILE* 5.3 0.2 - - + -
312B TRP* 1.3 77.2 - - - +
314B SER* 1.3 74.6 + - - +
315B GLN* 5.0 9.7 - - - +
325B ARG* 4.9 5.5 - - - +
326B GLN* 4.0 24.6 + - - +
504B ILE* 6.1 1.8 - - + -
549B THR* 3.3 39.9 + - + -
550B HIS* 4.4 9.5 + - - +
551B SER* 3.3 41.2 + - - +
554B TRP* 3.6 23.2 - - + -
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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