Contacts of the strand formed by residues 307 - 310 (chain A) in PDB entry 4TMU
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 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TYR* 3.7 19.3 - + - +
231A VAL* 4.9 7.0 - - + -
234A GLN* 3.6 39.5 - - + +
237A LYS* 3.2 30.5 - - + -
238A SER 3.7 4.3 - - - -
239A GLY* 3.0 25.2 - - - -
240A ILE 2.9 27.7 + - - -
241A ILE* 4.6 7.0 - - + -
288A GLN* 4.7 0.4 - - - -
289A ILE* 4.0 23.8 - - + -
305A VAL* 3.4 5.3 - - - +
306A ARG* 1.3 82.6 - - - +
308A VAL* 1.3 63.8 + - - +
309A VAL* 3.9 24.2 - - + -
327A ALA* 4.7 0.2 - - - -
335A GLU* 3.2 10.1 - - + +
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Residues in contact with VAL 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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240A ILE* 3.4 14.1 - - + +
242A TYR* 3.8 24.9 - - + -
305A VAL* 4.3 7.4 - - + -
307A PHE* 1.3 77.5 - - - +
309A VAL* 1.3 62.9 + - - +
310A HIS* 4.0 17.9 + - + -
323A GLU 3.5 27.4 - - - +
324A THR* 4.0 9.4 - - + +
326A ARG 4.6 1.3 - - - -
327A ALA* 3.8 25.3 - - + +
335A GLU 3.0 7.9 + - - +
336A ALA* 3.3 4.6 - - - +
337A MET* 2.9 24.6 + - - +
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Residues in contact with VAL 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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227A LEU* 3.9 15.9 - - + -
230A TYR* 3.6 36.8 - - + -
240A ILE 2.7 13.8 + - - +
241A ILE* 3.3 12.5 - - + -
242A TYR* 2.7 36.0 + - - +
307A PHE* 3.9 12.8 - - + -
308A VAL* 1.3 76.6 - - - +
310A HIS* 1.3 64.0 + - - +
311A PHE* 3.9 3.6 - - - +
337A MET* 3.3 8.5 - - + +
339A PHE* 3.5 29.4 - - + -
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Residues in contact with HIS 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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242A TYR* 3.8 17.1 - - + -
308A VAL* 4.0 10.2 + - + +
309A VAL* 1.3 72.3 - - - +
311A PHE* 1.3 62.9 + - - +
312A ASP 3.3 12.3 + - - +
314A PRO* 3.5 22.1 - - + +
320A TYR* 3.8 19.6 - + - -
323A GLU* 2.9 39.0 + - + +
324A THR* 3.6 28.5 - - + +
337A MET 2.9 11.0 + - - +
338A LEU* 3.6 17.6 - - + +
339A PHE* 2.9 27.2 + - - +
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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