Contacts of the strand formed by residues 302 - 310 (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 VAL 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 4.0 15.9 - - + -
163B LEU* 4.2 9.4 - - + -
197B LEU* 4.0 24.0 - - + -
200B VAL* 4.1 8.3 - - + -
296B ILE* 5.7 0.4 - - - -
300B GLY 4.1 6.7 - - - +
301B CYS* 1.3 79.4 - - - +
303B LEU* 1.3 71.6 + - - +
352B SER* 4.0 8.5 - - - -
353B LEU 3.3 9.9 - - - +
354B THR* 3.9 19.3 - - + +
355B CYS* 4.8 0.9 - - - -
383B VAL* 3.5 3.7 - - - -
384B LEU* 2.7 55.1 + - + +
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Residues in contact with LEU 303 (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* 4.0 18.8 - - + -
296B ILE* 4.6 3.8 - - + -
302B VAL* 1.3 73.4 - - - +
304B ARG* 1.3 58.6 + - - +
305B TRP* 3.5 13.0 - - + -
318B VAL* 4.9 3.1 - - + -
352B SER* 3.0 5.7 - - - -
353B LEU* 2.9 35.1 + - + +
355B CYS* 3.9 14.9 - - - -
361B TYR* 3.8 30.5 - - + +
363B LEU* 3.6 27.6 - - + -
381B VAL* 3.8 21.8 - - + -
382B GLU 3.5 13.2 - - - +
383B VAL* 4.1 11.4 - - + -
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Residues in contact with ARG 304 (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* 2.9 34.1 + - - -
164B TRP* 5.0 1.8 - - - +
165B LYS* 3.9 37.1 - - - +
168B VAL* 4.1 11.9 - - - +
204B LEU* 4.3 9.5 - - - +
302B VAL* 3.9 0.4 + - + -
303B LEU* 1.3 73.4 - - - +
305B TRP* 1.3 68.6 + - - +
351B GLY 3.5 11.2 - - - +
352B SER* 4.2 8.3 - - - -
380B THR 3.9 0.7 - - - +
381B VAL* 3.4 3.4 - - - +
382B GLU* 2.9 69.7 + - - +
384B LEU* 4.0 39.2 - - + +
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Residues in contact with TRP 305 (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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303B LEU* 3.5 35.9 - - + -
304B ARG* 1.3 80.5 - - - +
306B GLN* 1.3 65.0 + - - +
307B PHE* 4.0 17.7 - + + -
316B PHE* 3.6 28.6 - + - -
318B VAL* 4.3 16.2 - - + -
337B LEU* 4.2 12.8 - - + -
350B ASP* 3.3 6.4 - - - +
351B GLY* 2.9 42.4 + - - +
352B SER* 3.6 27.1 - - - -
353B LEU* 3.9 12.8 - - + -
363B LEU* 3.8 28.9 - - + -
365B PHE* 6.3 0.4 - - + -
380B THR 3.2 11.0 - - - +
381B VAL* 4.1 2.5 - - + -
502B EDO 4.4 1.8 - - - -
503B EDO 3.2 23.3 + - - -
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Residues in contact with GLN 306 (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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164B TRP* 5.8 1.6 + - - -
165B LYS* 3.6 36.8 - - - +
166B PRO* 5.0 4.5 - - - +
276B LEU* 4.2 12.6 - - - +
277B GLN 3.1 26.9 + - - -
278B TYR* 3.9 15.3 - - + +
305B TRP* 1.3 76.8 - - - +
307B PHE* 1.3 64.1 + - - +
349B GLU 3.2 13.5 - - - +
350B ASP* 4.1 8.9 - - + +
379B TYR* 3.3 3.5 - - - +
380B THR* 3.0 47.7 + - - +
381B VAL* 5.7 0.2 - - - +
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Residues in contact with PHE 307 (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* 3.9 6.3 - - - -
305B TRP* 4.0 13.7 - + + -
306B GLN* 1.3 78.0 - - - +
308B ALA* 1.3 60.6 + - - +
314B ILE* 3.8 20.0 - - + -
316B PHE* 3.8 37.7 - + + -
342B TYR* 4.3 7.0 - + + -
344B ALA* 3.8 19.4 - - + +
348B PRO* 3.7 3.1 - - - +
349B GLU* 2.9 63.6 + - + +
365B PHE* 3.7 30.1 - + + -
377B LEU* 4.3 4.3 - - + -
378B SER 3.0 14.1 - - - +
379B TYR* 4.0 4.9 - - + -
503B EDO 4.0 10.1 - - - -
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Residues in contact with ALA 308 (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 26.2 - - + +
307B PHE* 1.3 74.1 - - - +
309B SER* 1.3 62.0 + - - +
344B ALA* 3.6 14.1 - - - +
348B PRO* 4.6 5.2 - - + -
377B LEU* 3.5 9.5 - - - +
378B SER* 2.8 37.3 + - - +
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Residues in contact with SER 309 (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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308B ALA* 1.3 76.9 - - - +
310B ASP* 1.3 61.4 + - - +
312B GLY 2.7 18.7 + - - -
313B ASP* 4.2 1.4 - - - -
314B ILE* 4.2 20.2 - - - -
344B ALA* 2.9 17.9 + - - +
345B HIS* 2.6 46.4 + - - +
375B LYS* 5.4 4.3 - - - -
376B LYS 3.2 6.5 - - - -
377B LEU* 4.9 2.2 - - - -
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Residues in contact with ASP 310 (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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309B SER* 1.3 74.0 - - - +
311B GLY* 1.3 59.7 + - - +
312B GLY 3.5 2.4 + - - -
345B HIS* 4.9 0.7 - - - -
375B LYS* 3.2 7.6 - - - +
376B LYS* 2.5 59.2 + - + +
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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