Contacts of the strand formed by residues 305 - 310 (chain A) in PDB entry 6F3T
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 PHE 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLN 4.7 2.0 - - - -
241A TYR* 4.2 15.9 - + - -
242A PRO* 3.5 38.6 - - + -
246A HIS* 4.4 8.1 - - - +
275A TYR* 5.1 5.2 - - - -
300A PHE* 3.9 11.2 - + + -
303A SER 3.5 2.4 + - - -
304A LYS* 1.3 69.9 - - - +
306A VAL* 1.3 77.6 + - - +
307A LEU* 4.6 9.1 - - + +
336A HIS 3.0 8.9 + - - +
337A LEU* 3.4 20.9 - - + +
338A TYR 2.8 24.1 + - - +
357A GLY 6.4 0.2 - - - -
358A SER 3.8 9.2 - - - -
359A LEU 3.4 21.1 - - - -
360A ALA* 3.8 4.5 - - - +
361A GLY* 3.3 27.1 - - - -
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Residues in contact with VAL 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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304A LYS 4.0 9.6 - - - +
305A PHE* 1.3 92.0 - - - +
307A LEU* 1.3 64.1 + - - +
308A ARG* 4.6 0.7 - - + -
338A TYR* 3.3 14.8 - - + +
340A ASP* 4.4 7.6 - - + -
360A ALA 3.4 9.5 + - - +
362A GLU* 3.1 44.2 + - + +
363A ALA 4.0 2.0 - - - +
364A LYS* 3.8 50.5 - - + +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLU 5.0 0.2 - - - +
238A GLN* 3.5 39.5 - - + +
239A LEU* 3.6 34.1 - - + -
242A PRO* 4.3 10.5 - - + -
305A PHE* 4.6 6.5 - - + +
306A VAL* 1.3 77.1 - - - +
308A ARG* 1.3 58.8 + - - +
309A ILE* 3.5 30.7 - - + -
337A LEU* 4.6 5.4 - - + -
338A TYR 2.9 11.2 + - - +
339A ILE* 3.3 20.4 - - + +
340A ASP 2.7 31.1 + - - -
362A GLU* 5.2 1.6 - - - -
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Residues in contact with ARG 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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235A GLU* 4.5 0.3 - - - +
238A GLN* 3.0 22.1 + - - -
306A VAL* 4.6 1.8 - - + -
307A LEU* 1.3 74.5 - - - +
309A ILE* 1.3 60.8 + - - +
340A ASP* 3.0 32.3 + - + +
341A ILE 5.1 0.8 + - - -
342A PHE* 3.7 23.7 - - + +
347A ARG* 3.1 26.2 + - - +
362A GLU* 3.6 33.2 + - + +
363A ALA 3.5 20.7 + - - +
365A ARG* 3.6 23.5 - - - +
756A THR 3.0 27.9 + - - -
757A GLY* 3.8 14.4 + - - -
758A HIS* 4.0 14.5 - - - +
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Residues in contact with ILE 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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235A GLU* 3.8 24.9 - - + +
236A LEU* 4.6 4.5 - - + +
238A GLN* 3.4 17.3 - - - +
307A LEU* 3.5 15.3 - - + -
308A ARG* 1.3 79.6 - - - +
310A SER* 1.3 63.9 + - - +
313A SER* 4.3 4.9 - - - -
314A TYR* 3.6 37.7 - - + +
317A LEU* 4.5 13.5 - - + -
339A ILE* 3.6 27.1 - - + -
340A ASP 3.4 3.0 + - - -
341A ILE* 3.3 7.4 - - + -
342A PHE* 3.0 30.6 + - - -
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Residues in contact with SER 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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235A GLU* 2.8 23.1 + - - -
309A ILE* 1.3 79.0 - - - +
311A ARG* 1.3 64.9 + - - +
312A ASP* 3.6 3.2 + - - +
313A SER* 3.2 14.0 + - - -
314A TYR* 2.9 21.1 + - - +
341A ILE* 4.1 0.9 - - - -
342A PHE* 3.3 29.4 - - - -
344A GLY 3.5 17.5 - - - -
346A PRO* 3.7 15.4 - - - +
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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