Contacts of the strand formed by residues 302 - 310 (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 VAL 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.8 31.2 - - + -
163A LEU* 4.3 3.6 - - + -
197A LEU* 4.1 15.7 - - + -
200A VAL* 4.2 7.2 - - + -
300A GLY 3.9 8.5 - - - +
301A CYS* 1.3 78.6 - - - +
303A LEU* 1.3 72.5 + - - +
352A SER* 4.2 8.3 - - - -
353A LEU 3.3 11.9 - - - +
354A THR* 4.2 8.5 - - + +
355A CYS* 4.8 0.4 - - - -
382A GLU 3.7 0.3 - - - +
383A VAL* 3.5 3.3 - - - -
384A LEU* 2.7 61.8 + - + +
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Residues in contact with LEU 303 (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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294A ASN* 4.4 16.6 - - + +
296A ILE* 4.8 2.5 - - + -
301A CYS 4.3 0.4 + - - -
302A VAL* 1.3 73.4 - - - +
304A ARG* 1.3 59.3 + - - +
305A TRP* 3.7 12.0 - - + -
318A VAL* 4.6 2.2 - - + -
352A SER* 3.0 6.6 - - - -
353A LEU* 2.9 43.3 + - + +
355A CYS* 3.9 13.6 - - - -
361A TYR* 3.6 39.5 - - + -
363A LEU* 4.1 18.4 - - + -
381A VAL* 4.4 11.0 - - + -
382A GLU 3.5 5.4 - - - +
383A VAL* 3.9 26.7 - - + -
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Residues in contact with ARG 304 (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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163A LEU* 2.8 37.0 + - - -
165A LYS* 3.6 38.8 - - + +
168A VAL* 4.0 13.5 - - - +
204A LEU* 4.3 17.2 - - - +
302A VAL 4.0 0.2 + - - -
303A LEU* 1.3 76.0 - - - +
305A TRP* 1.3 68.2 + - - +
351A GLY 3.4 12.6 - - - +
352A SER* 4.2 6.1 - - - -
380A THR* 4.0 0.9 - - - +
381A VAL* 3.6 2.6 - - - +
382A GLU* 2.9 68.7 + - + +
384A LEU* 4.1 31.8 - - + +
503A EDO 4.1 14.6 - - - +
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Residues in contact with TRP 305 (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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303A LEU* 3.7 17.5 - - + -
304A ARG* 1.3 80.1 - - - +
306A GLN* 1.3 63.9 + - - +
307A PHE* 3.8 15.3 - + + -
316A PHE* 3.4 33.1 - + - -
318A VAL* 4.3 6.3 - - + -
337A LEU* 4.0 15.7 - - + -
350A ASP* 3.2 7.7 - - - +
351A GLY* 3.0 49.7 + - - +
352A SER* 3.5 31.2 - - - -
353A LEU* 3.9 24.5 - - + -
363A LEU* 3.7 27.4 - - + -
365A PHE* 6.1 0.4 - - + -
380A THR 3.2 11.7 - - - +
381A VAL* 4.2 2.9 - - + -
504A EDO 2.9 28.2 + - - -
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Residues in contact with GLN 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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165A LYS* 3.5 33.2 - - - +
166A PRO* 5.0 0.7 - - - +
276A LEU* 3.8 24.7 - - + +
277A GLN 2.8 28.7 + - - -
278A TYR* 3.9 5.9 - - + -
305A TRP* 1.3 77.5 - - - +
307A PHE* 1.3 66.5 + - - +
349A GLU 3.1 13.5 - - - +
350A ASP* 3.8 9.8 - - + +
379A TYR* 3.3 2.1 - - - +
380A THR* 3.0 44.1 + - - +
381A VAL* 5.7 0.2 - - - +
511A EDO 3.0 19.4 + - - -
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Residues in contact with PHE 307 (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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278A TYR* 3.8 6.6 - - - -
305A TRP* 3.8 20.6 - + + -
306A GLN* 1.3 79.2 - - - +
308A ALA* 1.3 60.1 + - - +
314A ILE* 3.8 25.6 - - + -
316A PHE* 3.6 39.3 - + + -
342A TYR* 4.4 5.8 - + + -
344A ALA* 3.9 13.5 - - + +
348A PRO* 3.5 4.0 - - - +
349A GLU* 2.8 63.5 + - + -
365A PHE* 3.6 23.1 - + + -
377A LEU* 4.2 4.5 - - + -
378A SER 3.2 13.0 - - - +
379A TYR* 3.9 9.6 - - + -
504A EDO 4.1 1.3 - - - -
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Residues in contact with ALA 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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278A TYR* 3.5 27.3 - - + +
307A PHE* 1.3 75.5 - - - +
309A SER* 1.3 62.7 + - - +
344A ALA* 3.4 16.2 - - - +
348A PRO* 4.5 6.3 - - + -
377A LEU* 3.4 8.9 - - - +
378A SER* 2.9 33.7 + - - +
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Residues in contact with SER 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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308A ALA* 1.3 76.1 - - - +
310A ASP* 1.3 63.7 + - - +
312A GLY 2.9 23.3 + - - -
313A ASP 4.0 4.1 - - - -
314A ILE* 4.3 18.8 - - - -
344A ALA* 3.1 14.0 + - - +
345A HIS* 3.1 35.6 + - - +
375A LYS* 5.0 4.7 - - - -
376A LYS 3.2 10.1 - - - -
377A LEU* 4.7 2.9 - - - -
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Residues in contact with ASP 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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309A SER* 1.3 76.1 - - - +
311A GLY* 1.3 67.4 + - - +
312A GLY 3.5 2.9 - - - +
345A HIS* 4.6 2.4 - - - +
375A LYS* 3.5 7.4 - - - +
376A LYS* 2.8 51.2 + - + +
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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