Contacts of the strand formed by residues 359 - 366 (chain B) 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 GLY 359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B GLU* 3.6 3.2 - - - -
296B ILE* 2.8 36.3 + - - +
320B LEU* 4.1 11.7 - - - -
321B LYS 5.7 1.3 - - - -
324B MET* 6.1 5.8 - - - -
357B GLN* 3.4 2.6 + - - -
358B ALA* 1.3 74.3 - - - +
360B VAL* 1.3 64.8 + - - -
361B TYR* 3.8 2.1 + - - -
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Residues in contact with VAL 360 (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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293B GLU* 3.9 29.6 - - + +
294B ASN 3.6 9.0 - - - +
295B GLU* 4.2 20.6 - - + +
320B LEU* 3.5 8.1 - - - +
321B LYS* 3.0 63.9 + - + +
324B MET* 4.3 26.4 - - + +
359B GLY* 1.3 73.0 - - - +
361B TYR* 1.3 61.1 + - - +
362B VAL* 3.8 3.2 + - + -
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Residues in contact with TYR 361 (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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292B VAL 3.7 1.7 - - - +
293B GLU 3.7 0.7 - - - -
294B ASN* 2.9 40.0 + - - +
296B ILE* 3.5 21.3 - - + -
303B LEU* 3.8 18.8 - - + -
318B VAL* 4.3 9.0 - - + -
319B PHE 3.4 7.2 - - - +
320B LEU* 3.8 21.2 - - + +
336B VAL* 4.5 13.5 - - + -
353B LEU* 4.0 25.8 - - + -
355B CYS* 3.7 23.8 - - + -
356B LEU* 3.5 8.8 + - - +
357B GLN* 3.0 46.7 + - - +
359B GLY 3.9 3.6 - - - -
360B VAL* 1.3 75.6 - - - +
362B VAL* 1.3 60.1 + - - +
363B LEU* 4.1 2.8 + - - +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLN* 3.7 40.8 - - + +
292B VAL 3.4 6.3 - - - +
293B GLU* 4.0 18.6 - - + -
318B VAL* 3.2 5.5 - - - -
319B PHE* 2.7 40.0 + - + +
321B LYS* 4.1 7.4 - - + -
333B MET* 4.0 30.3 - - + -
360B VAL* 4.1 10.1 - - + +
361B TYR* 1.3 76.6 - - - +
363B LEU* 1.3 72.2 + - - +
364B ARG* 3.5 4.6 + - + +
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Residues in contact with LEU 363 (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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290B LEU 3.5 4.0 - - - +
291B GLN* 3.6 0.3 - - - -
292B VAL* 2.9 41.6 + - + +
294B ASN* 5.6 1.1 - - - +
303B LEU* 3.6 29.6 - - + -
305B TRP* 3.8 20.0 - - + -
316B PHE* 3.5 32.5 - - + -
317B GLY 3.6 2.7 - - - -
318B VAL* 4.1 12.3 - - + -
361B TYR 4.8 1.1 - - - +
362B VAL* 1.3 76.1 - - - +
364B ARG* 1.3 59.5 + - - +
365B PHE* 3.7 14.4 + - + -
381B VAL* 3.5 35.0 - - + -
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Residues in contact with ARG 364 (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 SER* 4.5 15.3 + - - -
290B LEU 3.5 9.0 - - - +
291B GLN* 4.8 15.2 - - + +
315B GLY 3.7 0.5 - - - +
316B PHE* 3.5 5.5 - - - -
317B GLY 2.9 31.1 + - - +
319B PHE* 3.9 39.5 - - + -
330B ALA* 4.1 22.2 - - - +
333B MET* 5.4 1.8 - - - -
339B SER* 4.5 11.6 + - - -
362B VAL* 3.5 7.3 + - + -
363B LEU* 1.3 70.1 - - - +
365B PHE* 1.3 66.4 + - - +
366B ASP* 3.7 37.8 + - - +
368B THR* 4.4 12.7 + - - +
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Residues in contact with PHE 365 (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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284B VAL* 5.1 3.2 - - + +
289B SER* 3.3 7.8 - - - -
290B LEU* 3.0 48.6 + - + +
292B VAL* 4.2 17.9 - - + -
305B TRP* 6.3 0.4 - - + -
307B PHE* 3.7 26.5 - + + -
314B ILE* 4.3 15.5 - - + -
315B GLY 3.3 5.8 - - - +
316B PHE* 3.7 30.1 - + + -
363B LEU* 4.1 23.3 - - + -
364B ARG* 1.3 71.2 - - - +
366B ASP* 1.3 58.6 + - - +
367B ASN 4.1 0.2 - - - -
377B LEU* 3.3 42.4 - - + -
379B TYR* 4.2 20.6 - + + -
381B VAL* 5.5 1.3 - - + -
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Residues in contact with ASP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER* 4.4 2.9 - - - -
314B ILE* 3.4 4.8 - - - +
315B GLY* 2.7 46.7 + - - +
339B SER* 4.2 9.9 + - - +
364B ARG* 3.8 29.3 + - - +
365B PHE* 1.3 72.2 - - - +
367B ASN* 1.3 59.5 + - - +
368B THR* 2.4 44.8 + - - +
369B TYR* 3.2 18.3 - - - -
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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