Contacts of the strand formed by residues 334 - 342 (chain A) in PDB entry 4TLG
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A PHE* 3.1 7.3 - - - -
320A LEU* 2.8 56.9 + - + +
322A THR* 3.7 17.1 - - - +
333A MET* 1.3 71.1 - - - +
335A GLU* 1.3 72.5 + - - +
336A VAL* 3.4 3.5 + - + -
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Residues in contact with GLU 335 (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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319A PHE* 3.9 25.2 - - + -
333A MET 3.6 3.4 + - - +
334A THR* 1.3 78.5 - - - +
336A VAL* 1.3 61.3 + - - +
337A LEU 4.2 2.7 - - - +
338A PRO* 3.5 47.7 - - + +
339A SER 4.6 2.1 + - - -
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Residues in contact with VAL 336 (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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318A VAL* 2.8 18.4 + - + +
319A PHE 3.9 9.4 - - - -
320A LEU* 3.8 32.3 - - + +
334A THR* 4.0 4.0 - - + +
335A GLU* 1.3 75.9 - - - +
337A LEU* 1.3 57.0 + - - +
338A PRO* 4.2 5.0 - - - +
353A LEU* 4.0 26.9 - - + -
361A TYR* 4.2 18.6 - - + -
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Residues in contact with LEU 337 (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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305A TRP* 4.0 29.6 - - + -
316A PHE* 4.2 11.0 - - + +
317A GLY* 3.5 1.0 - - - -
318A VAL* 3.0 45.9 + - + +
319A PHE* 5.0 0.5 - - - -
335A GLU* 4.2 3.1 - - - +
336A VAL* 1.3 76.2 - - + +
338A PRO* 1.3 85.1 - - + +
339A SER 3.4 1.2 + - - -
340A GLN* 6.0 3.6 - - - +
342A TYR* 5.3 4.0 - - - +
353A LEU* 4.6 7.4 - - + -
504A EDO 4.6 13.0 - - - +
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Residues in contact with PRO 338 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A PHE 3.9 3.8 - - - +
335A GLU* 3.5 33.6 - - - +
336A VAL 4.2 4.7 - - - +
337A LEU* 1.3 99.2 - - + +
339A SER* 1.3 66.8 + - - +
340A GLN* 3.6 17.7 + - + +
342A TYR* 4.9 1.6 + - - -
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Residues in contact with SER 339 (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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315A GLY 4.1 0.7 - - - -
316A PHE 3.2 24.1 + - - -
317A GLY* 3.6 6.6 + - - -
319A PHE* 4.5 16.5 - - - -
335A GLU* 4.6 3.4 + - - -
337A LEU 3.4 2.8 + - - -
338A PRO* 1.3 75.1 - - - +
340A GLN* 1.3 64.0 + - - +
364A ARG* 4.3 10.3 + - - -
366A ASP* 4.4 0.7 - - - +
510A EDO 2.5 38.4 + - - -
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Residues in contact with GLN 340 (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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316A PHE 2.9 26.0 + - - -
337A LEU* 6.0 3.6 - - - +
338A PRO* 3.8 15.2 + - + +
339A SER* 1.3 81.7 - - - +
341A ARG* 1.3 64.5 + - - +
342A TYR* 3.3 37.2 + - + +
510A EDO 3.8 11.0 - - - -
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Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A ASP* 2.8 37.1 + - - +
314A ILE 3.6 4.5 - - - +
315A GLY* 4.4 0.2 - - - -
340A GLN* 1.3 78.8 - - - +
342A TYR* 1.3 65.3 + - - +
369A TYR* 3.4 56.2 - - + +
510A EDO 3.9 15.4 + - - +
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Residues in contact with TYR 342 (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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307A PHE* 4.4 4.5 - + + -
313A ASP* 3.2 18.7 - - - +
314A ILE 2.9 18.9 + - - +
316A PHE* 3.7 32.0 + - + -
337A LEU* 5.3 4.2 - - - +
338A PRO 4.9 2.1 + - - -
340A GLN* 3.3 54.2 + - + +
341A ARG* 1.3 76.5 - - - +
343A ASN* 1.3 59.3 + - - +
344A ALA* 2.9 13.7 + - + +
349A GLU* 3.4 38.6 - - + +
504A EDO 3.4 35.4 - - - -
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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