Contacts of the helix formed by residues 270 - 281 (chain I) 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 GLY 270 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144I PRO* 4.0 9.4 - - - +
165I LEU* 3.6 39.2 - - - +
269I LEU* 1.3 76.7 - - - +
271I GLU* 1.3 55.2 + - - -
272I ALA* 3.1 3.6 - - - -
273I GLY 2.7 4.5 + - - -
274I ARG* 2.6 33.1 + - - +
288I ARG* 4.6 2.2 - - - -
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Residues in contact with GLU 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I VAL* 5.5 6.2 - - - +
269I LEU 3.6 1.4 + - - -
270I GLY* 1.3 69.6 - - - -
272I ALA* 1.3 56.3 + - - +
274I ARG* 3.8 27.8 + - - +
275I TYR* 2.9 37.1 + - + +
288I ARG* 3.4 36.8 + - - +
464I LEU* 3.7 20.6 - - + -
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Residues in contact with ALA 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I SER* 5.1 1.8 - - - -
144I PRO* 5.0 1.1 - - + -
270I GLY* 3.1 1.1 - - - -
271I GLU* 1.3 78.1 - - - +
273I GLY* 1.3 59.2 + - - +
275I TYR* 4.4 2.7 - - - -
276I LYS* 2.9 34.0 + - - +
332I ARG* 3.9 17.9 - - - +
464I LEU* 3.1 48.2 - - + +
466I PHE* 5.0 10.2 - - + -
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Residues in contact with GLY 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I PRO* 3.4 38.8 - - - +
145I GLY* 3.6 1.3 - - - -
269I LEU* 3.5 8.1 - - - -
270I GLY 2.7 15.0 + - - -
272I ALA* 1.3 71.9 - - - +
274I ARG* 1.3 58.3 + - - -
276I LYS* 4.8 0.2 - - - -
277I ALA* 2.9 35.7 + - - +
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Residues in contact with ARG 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I LEU* 3.5 15.6 - - + +
270I GLY 2.6 18.5 + - - +
271I GLU* 3.8 25.1 + - - +
273I GLY* 1.3 70.7 - - - +
275I TYR* 1.3 67.3 + - - +
277I ALA* 3.8 2.2 - - - +
278I GLU* 2.9 54.0 + - - +
285I LEU* 2.7 55.8 + - + +
286I SER* 3.4 16.1 + - - +
287I GLY 3.7 13.6 + - - +
288I ARG* 4.7 9.0 - - + +
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Residues in contact with TYR 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271I GLU* 2.9 23.1 + - + +
272I ALA* 4.0 3.4 - - - +
274I ARG* 1.3 89.2 - - - +
276I LYS* 1.3 63.1 + - + +
278I GLU* 3.1 11.6 + - + +
279I GLU* 3.0 63.2 + - + +
464I LEU* 3.7 29.4 - - + -
466I PHE* 6.0 5.8 - + - -
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Residues in contact with LYS 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I SER* 4.0 2.9 - - - +
144I PRO 3.2 21.4 + - - -
145I GLY* 3.9 5.7 - - - -
146I VAL 4.1 0.2 + - - -
147I TYR* 3.3 31.9 + - - -
272I ALA 2.9 22.3 + - - +
275I TYR* 1.3 76.9 - - + +
277I ALA* 1.3 63.6 + - - +
279I GLU* 3.3 18.4 - - + +
280I LYS* 2.9 58.8 + - + +
329I GLY 3.9 7.0 - - - +
330I ASN* 3.9 7.4 - - - +
466I PHE* 3.5 35.9 - - + -
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Residues in contact with ALA 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I GLY* 3.7 19.5 - - - -
146I VAL* 3.7 18.4 - - + +
269I LEU* 5.7 1.6 - - + -
273I GLY 2.9 20.0 + - - +
274I ARG* 4.1 2.9 - - - +
276I LYS* 1.3 77.8 - - - +
278I GLU* 1.3 62.0 + - - +
280I LYS* 3.6 10.8 - - - -
281I LEU* 3.2 35.0 + - + +
285I LEU* 6.2 2.7 - - + -
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Residues in contact with GLU 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I ARG* 2.9 53.5 + - - +
275I TYR* 3.1 11.0 + - + +
277I ALA* 1.3 78.7 - - - +
279I GLU* 1.3 61.0 + - + +
282I GLY* 3.6 1.2 + - - -
283I VAL* 2.8 50.2 + - - +
284I GLY* 3.4 22.4 - - - -
285I LEU* 3.8 12.3 + - + +
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Residues in contact with GLU 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I TYR* 3.0 58.9 + - + +
276I LYS* 3.3 19.2 - - + +
278I GLU* 1.3 79.7 - - + +
280I LYS* 1.3 61.7 + - + +
281I LEU 3.4 0.2 - - - -
282I GLY* 3.7 9.3 + - - +
466I PHE* 5.8 1.4 - - - -
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Residues in contact with LYS 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I VAL* 3.2 34.8 - - + +
147I TYR* 4.9 0.2 - - - -
148I PHE* 3.5 20.5 - - + -
276I LYS* 2.9 44.0 + - + +
277I ALA* 3.6 10.5 - - - +
278I GLU 3.4 0.2 - - - -
279I GLU* 1.3 77.0 - - + +
281I LEU* 1.3 61.9 + - + +
282I GLY 3.4 0.4 + - - -
309I TYR* 3.1 30.4 + - - -
323I ASP* 3.6 25.8 + - - +
330I ASN* 4.7 6.3 + - - -
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Residues in contact with LEU 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I VAL* 3.6 26.0 - - + -
148I PHE* 3.6 20.9 - - + -
277I ALA* 3.2 26.2 + - + +
279I GLU 3.4 0.2 - - - -
280I LYS* 1.3 76.4 - - - +
282I GLY* 1.3 61.8 + - - +
283I VAL* 3.4 15.7 + - + +
301I GLU 6.0 0.2 - - - +
302I VAL* 4.8 5.4 - - + +
305I PRO* 3.8 25.8 - - + +
306I THR* 4.0 10.1 - - - +
308I ARG* 2.4 36.5 + - - +
309I TYR* 3.5 27.8 - - + -
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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