Contacts of the strand formed by residues 375 - 384 (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 LYS 375 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B SER* 3.4 4.8 - - - -
284B VAL* 2.7 47.5 + - + +
285B GLY 4.0 0.4 + - - -
309B SER* 5.4 4.3 - - - -
310B ASP 3.2 10.1 - - - +
312B GLY 5.3 3.1 - - - +
313B ASP 4.5 12.8 - - - +
314B ILE* 4.6 12.3 - - + -
367B ASN* 4.4 14.8 - - - +
374B ALA* 1.3 77.1 - - - +
376B LYS* 1.3 61.5 + - - +
377B LEU* 4.0 2.0 + - + +
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR* 5.3 7.9 - - + -
282B ARG 3.3 9.9 - - - +
283B SER* 4.5 2.7 - - - +
308B ALA 4.5 0.2 - - - -
309B SER* 3.2 5.2 - - - -
310B ASP* 2.5 59.5 + - + +
375B LYS* 1.3 74.1 - - - +
377B LEU* 1.3 59.4 + - - +
378B SER 4.2 0.4 + - - -
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B HIS 3.9 0.5 - - - +
281B THR* 3.2 4.3 - - - -
282B ARG* 2.6 45.9 + - + +
284B VAL* 4.6 14.4 - - + -
290B LEU* 4.0 17.0 - - + -
307B PHE* 4.3 8.3 - - + -
308B ALA 3.5 14.8 - - - +
309B SER* 4.9 1.8 - - - -
314B ILE* 4.4 16.4 - - + -
365B PHE* 3.3 61.0 - - + -
375B LYS* 4.0 3.3 + - + +
376B LYS* 1.3 73.2 - - - +
378B SER* 1.3 62.4 + - - +
379B TYR* 4.1 13.1 + - + -
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.6 30.7 - - - -
280B HIS 3.2 5.4 - - - -
281B THR* 3.9 17.7 - - - +
307B PHE* 3.0 7.4 - - - +
308B ALA* 2.8 40.3 + - - +
376B LYS 4.2 1.0 + - - -
377B LEU* 1.3 72.9 - - - +
379B TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 379 (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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278B TYR* 3.7 5.6 - - - -
279B GLU* 3.4 2.3 + - - -
280B HIS* 2.8 77.8 + + + +
282B ARG* 3.9 34.5 + - + -
290B LEU* 4.4 11.5 - - + +
292B VAL* 3.9 33.5 - - + +
306B GLN 3.3 11.4 - - - +
307B PHE* 4.0 8.7 - - + -
365B PHE* 4.2 11.2 - + + -
377B LEU* 4.1 18.8 - - + -
378B SER* 1.3 75.9 - - - +
380B THR* 1.3 63.7 + - - +
381B VAL* 4.1 17.3 - - + -
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Residues in contact with THR 380 (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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165B LYS* 4.8 7.4 - - + +
277B GLN 4.0 4.7 + - - -
278B TYR* 3.3 9.7 - - - -
279B GLU* 3.0 48.7 + - + +
280B HIS* 5.4 0.2 - - - -
304B ARG 3.9 0.4 - - - +
305B TRP* 3.2 4.3 - - - -
306B GLN* 3.0 48.6 + - + +
379B TYR* 1.3 71.1 - - - +
381B VAL* 1.3 65.6 + - - +
382B GLU* 3.9 25.6 - - + +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLU* 4.4 7.9 + - - +
280B HIS* 5.9 1.0 - - - -
292B VAL* 4.5 10.5 - - + -
294B ASN* 3.2 31.8 + - - +
303B LEU* 3.8 19.1 - - + -
304B ARG 3.4 7.4 - - - +
305B TRP* 4.1 3.1 - - + -
363B LEU* 3.5 34.5 - - + -
365B PHE* 5.5 2.2 - - + -
379B TYR* 4.1 20.9 - - + -
380B THR* 1.3 80.2 - - - +
382B GLU* 1.3 69.0 + - - +
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Residues in contact with GLU 382 (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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165B LYS* 3.0 24.8 + - - +
279B GLU* 4.6 11.0 - - - +
294B ASN* 5.7 0.9 - - - -
302B VAL 3.7 0.3 - - - +
303B LEU* 3.5 7.0 - - - +
304B ARG* 2.9 66.3 + - - +
380B THR* 3.9 17.1 - - + +
381B VAL* 1.3 81.4 - - - +
383B VAL* 1.3 66.6 + - - +
384B LEU* 3.9 14.8 + - + +
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Residues in contact with VAL 383 (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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294B ASN* 4.2 17.5 + - + +
295B GLU 4.4 7.0 - - - +
296B ILE* 3.5 36.3 - - + -
301B CYS* 4.1 11.7 - - + -
302B VAL 3.5 4.0 - - - +
303B LEU* 4.1 10.1 - - + -
382B GLU* 1.3 74.8 - - - +
384B LEU* 1.3 65.8 + - - +
385B LEU* 4.0 26.4 + - + +
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Residues in contact with LEU 384 (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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163B LEU* 4.2 14.8 - - + -
200B VAL* 3.9 16.6 - - + +
204B LEU* 4.2 24.5 - - + -
301B CYS* 3.5 6.4 - - - -
302B VAL* 2.7 51.6 + - + +
304B ARG* 4.0 56.3 - - + +
382B GLU* 4.2 13.5 - - + +
383B VAL* 1.3 80.0 - - - +
385B LEU* 1.3 64.1 + - - +
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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