Contacts of the strand formed by residues 278 - 284 (chain D) in PDB entry 4XLN
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 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271D TYR* 4.5 16.6 - - + -
272D LEU 3.3 9.6 - - - +
273D ARG* 3.4 46.0 - - + +
277D GLU* 1.3 87.8 - - + +
279D VAL* 1.3 66.4 + - - +
280D ALA 4.5 3.8 - - - +
281D ARG* 3.6 34.1 - - - +
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Residues in contact with VAL 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D GLU* 3.3 40.6 - - + +
256D SER 3.4 12.1 - - - +
272D LEU* 2.4 23.0 + - + +
273D ARG 3.9 1.8 - - - -
274D GLN* 3.4 45.3 - - + +
277D GLU* 6.0 0.2 - - - -
278D VAL* 1.3 77.3 - - - +
280D ALA* 1.3 59.8 + - - +
281D ARG* 5.6 0.5 + - - -
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Residues in contact with ALA 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D GLU* 4.6 10.1 - - + -
271D TYR* 3.8 1.0 - - - -
272D LEU* 2.8 29.7 + - + +
278D VAL* 3.7 2.6 - - - +
279D VAL* 1.3 84.1 - - + +
281D ARG* 1.3 70.8 + - - +
282D TYR* 3.6 33.7 - - + +
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Residues in contact with ARG 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D GLU* 2.9 31.7 + - + +
220D ARG* 3.0 50.8 + - - +
221D ALA* 3.5 3.6 - - + -
222D ALA* 3.1 21.1 + - - +
269D LEU* 6.3 1.3 - - + -
270D ILE 3.5 4.0 - - - +
271D TYR* 3.6 28.3 - - + -
278D VAL* 3.6 24.9 - - - +
279D VAL 5.6 0.2 + - - -
280D ALA* 1.3 82.0 - - - +
282D TYR* 1.3 66.7 + - - +
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Residues in contact with TYR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ALA* 4.4 0.7 - - - -
222D ALA* 3.2 27.6 - - + +
251D PHE* 4.1 22.7 - + + -
253D ALA* 4.4 0.2 - - - -
254D GLU* 3.7 24.1 + - + +
255D GLU* 3.4 31.2 + - - +
269D LEU* 3.4 8.3 - - - +
270D ILE* 2.9 41.9 + - + +
272D LEU* 3.5 28.7 - - + -
280D ALA* 3.6 21.8 - - + +
281D ARG* 1.3 81.6 - - - +
283D PHE* 1.3 61.9 + - - +
284D LEU* 4.4 2.0 - - + +
304D LEU* 3.4 25.4 - - + -
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Residues in contact with PHE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ALA* 3.6 23.3 - - + +
222D ALA 3.1 10.0 + - - +
223D LEU* 3.4 37.7 - - + +
242D LEU* 4.2 8.1 - - + -
264D LEU* 6.3 0.4 - - + -
267D GLY* 6.1 0.2 - - - -
268D HIS 4.2 4.0 - - - -
269D LEU* 3.6 9.9 - - + -
282D TYR* 1.3 73.3 - - - +
284D LEU* 1.3 74.8 + - - +
285D PRO* 3.5 40.1 - - + +
313D LEU* 4.5 13.0 - - + -
314D PRO* 4.3 11.2 - - + -
317D MET* 4.1 22.0 - - + -
335D LEU* 4.1 26.0 - - + -
337D LEU* 3.5 14.1 - - + -
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D PHE* 4.6 10.8 - - + -
267D GLY* 3.6 2.4 - - - -
268D HIS* 2.9 64.8 + - + +
270D ILE* 4.0 26.2 - - + -
282D TYR* 4.4 5.8 - - + +
283D PHE* 1.3 87.4 - - - +
285D PRO* 1.3 65.1 - - - +
288D MET* 3.7 23.8 - - - +
290D PRO* 3.8 18.2 - - + -
304D LEU* 5.8 0.9 - - + -
305D ALA* 3.6 32.3 - - + -
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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