Contacts of the helix formed by residues 302 - 314 (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 VAL 302 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146I VAL* 5.1 5.4 - - + -
162I ILE* 3.9 22.7 - - + -
269I LEU* 5.7 2.5 - - + -
281I LEU* 4.8 4.4 - - + +
285I LEU* 3.9 17.0 - - + -
289I THR 3.8 9.2 - - - +
290I LEU* 3.2 52.5 - - + +
300I ASP* 3.1 3.0 + - - +
301I GLU* 1.3 82.7 - - - +
303I PHE* 1.3 72.5 + - + +
304I LEU 3.2 2.0 - - - -
305I PRO* 3.1 5.7 - - - +
306I THR* 3.0 22.9 + - + +
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Residues in contact with PHE 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I ILE* 4.7 9.6 - - + -
172I ILE* 4.1 12.8 - - + -
174I LEU* 6.3 2.2 - - + -
184I MET* 3.8 18.8 - - + -
196I LEU* 3.5 33.0 - - + -
197I LEU* 5.1 6.3 - - + -
200I LEU* 3.8 17.5 - - + -
261I LEU* 3.5 33.4 - - + -
290I LEU* 3.9 25.8 - - + -
291I VAL* 4.0 2.5 - - + -
300I ASP* 3.0 27.8 + - - +
302I VAL* 1.3 74.7 - - + +
304I LEU* 1.3 57.0 + - - +
306I THR* 3.2 10.3 - - + +
307I LEU* 2.9 34.0 + - - +
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Residues in contact with LEU 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I LEU* 5.1 8.1 - - + -
202I TYR* 3.5 37.9 - - + +
206I THR 6.0 2.0 - - - +
207I LEU* 5.8 2.9 - - + -
210I GLU* 5.1 9.9 - - - +
283I VAL* 6.4 0.4 - - + -
300I ASP* 2.7 20.4 + - - +
303I PHE* 1.3 73.9 - - - +
305I PRO* 1.4 69.9 - - + +
307I LEU* 3.9 5.9 - - + +
308I ARG* 2.9 35.7 + - + +
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Residues in contact with PRO 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I LEU* 3.8 11.9 - - + +
283I VAL* 3.5 46.0 - - + -
284I GLY 5.4 0.2 - - - +
301I GLU* 3.4 22.0 - - - +
302I VAL 3.1 20.2 - - - +
304I LEU* 1.4 94.2 - - + +
306I THR* 1.3 56.5 + - - +
308I ARG* 3.2 11.1 + - + +
309I TYR* 2.9 29.5 + - - +
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Residues in contact with THR 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146I VAL* 4.0 24.7 - - - +
148I PHE* 4.2 9.2 - - - -
160I ALA* 4.4 8.7 - - - +
162I ILE* 3.7 25.8 - - + +
174I LEU* 5.1 11.6 - - + +
281I LEU* 4.0 11.2 - - - +
302I VAL 3.0 16.7 + - - +
303I PHE* 3.2 21.5 - - + +
305I PRO* 1.3 74.4 - - - +
307I LEU* 1.3 65.5 + - + +
309I TYR* 4.0 1.0 - - - +
310I LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I LEU* 3.7 20.9 - - + -
193I LEU* 3.6 34.1 - - + -
197I LEU* 5.1 12.3 - - + -
211I LEU* 6.1 2.7 - - + -
221I LEU* 4.8 18.2 - - + -
303I PHE 2.9 19.3 + - - +
304I LEU* 3.9 6.7 - - + +
306I THR* 1.3 75.8 - - + +
308I ARG* 1.3 61.3 + - - +
310I LEU* 4.2 4.5 - - + -
311I PHE* 2.9 68.3 + - + +
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Residues in contact with ARG 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210I GLU* 5.3 9.6 - - - +
214I TYR* 3.2 29.6 + - - +
281I LEU* 2.4 36.9 + - - +
282I GLY* 4.1 5.3 - - - +
283I VAL* 4.3 10.0 - - - +
304I LEU* 2.9 22.2 + - + +
305I PRO* 3.2 13.6 + - + +
307I LEU* 1.3 78.9 - - - +
309I TYR* 1.3 80.8 + - - +
312I ALA* 2.9 27.4 + - - +
320I HIS* 3.4 24.6 + - - -
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Residues in contact with TYR 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I PHE* 3.3 41.2 - + + -
280I LYS* 3.1 30.5 + - - -
281I LEU* 3.5 23.1 - - + -
305I PRO 2.9 6.7 + - - +
306I THR 4.1 0.9 - - - +
308I ARG* 1.3 86.3 - - - +
310I LEU* 1.3 61.6 + - - +
312I ALA* 3.3 4.6 - - - +
313I LEU* 2.9 31.8 + - + +
319I GLY 3.5 7.7 + - - -
320I HIS* 3.2 34.9 - + + -
321I GLU 3.0 33.9 + - - -
323I ASP* 5.2 0.7 + - - -
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Residues in contact with LEU 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I PHE* 4.5 5.3 - - + -
158I TYR* 3.8 19.7 - - + +
159I ILE* 4.1 2.2 - - - +
160I ALA* 3.7 33.9 - - + +
174I LEU* 3.6 43.1 - - + +
176I VAL* 4.7 10.3 - - + -
306I THR 2.9 19.1 + - - +
307I LEU* 3.8 10.3 - - + +
309I TYR* 1.3 80.0 - - - +
311I PHE* 1.3 59.3 + - + +
313I LEU* 3.9 5.9 - - + +
314I THR* 2.8 49.5 + - + +
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Residues in contact with PHE 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I LEU* 5.9 0.2 - - + -
176I VAL* 5.7 6.7 - - + -
182I VAL* 5.9 2.9 - - + -
193I LEU* 4.8 7.9 - - + -
211I LEU* 3.5 32.1 - - + -
214I TYR* 3.5 24.1 - + + -
217I LEU* 3.5 38.2 - - + +
218I VAL* 4.7 2.2 - - - -
220I GLY* 5.3 5.4 - - - -
221I LEU* 5.0 12.1 - - + -
307I LEU* 2.9 59.0 + - + +
310I LEU* 1.3 84.3 - - + +
312I ALA* 1.3 59.3 + - - +
314I THR* 3.1 8.6 + - - -
315I ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 312 (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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214I TYR* 3.7 13.8 - - + -
308I ARG* 2.9 21.9 + - - +
309I TYR* 3.2 7.2 + - - +
311I PHE* 1.3 76.1 - - - +
313I LEU* 1.3 55.2 + - - +
315I ALA* 2.7 23.2 + - - +
316I GLY 3.3 1.4 + - - -
317I VAL* 3.1 26.1 - - + +
320I HIS* 3.5 32.5 - - + +
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Residues in contact with LEU 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I PHE* 3.7 32.5 - - + -
157I ARG* 4.7 0.3 + - - -
158I TYR* 3.5 40.3 - - + -
309I TYR* 2.9 20.9 + - + +
310I LEU* 3.9 7.6 - - + +
312I ALA* 1.3 72.7 - - - +
314I THR* 1.3 58.2 + - - +
316I GLY* 3.1 18.1 + - - +
320I HIS* 3.6 21.1 - - + +
321I GLU* 3.6 27.1 - - + -
322I VAL* 3.7 23.1 - - + +
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Residues in contact with THR 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I ARG* 2.8 63.0 + - + +
158I TYR* 3.7 20.4 - - + +
176I VAL* 6.1 2.9 - - + -
217I LEU* 3.3 19.1 - - - +
310I LEU* 2.8 38.9 + - + +
311I PHE* 3.1 16.0 + - - -
313I LEU* 1.3 75.4 - - + +
315I ALA* 1.3 57.0 + - - +
316I GLY 3.3 0.7 - - - -
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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