Contacts of the helix formed by residues 328 - 338 (chain B) in PDB entry 5IL2
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 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.8 8.3 - - + -
326B LYS 3.4 2.6 + - - -
327B PRO* 1.3 71.3 - - - +
329B GLU* 1.3 66.5 + - - +
330B ILE 3.1 0.4 - - - -
331B PHE* 2.9 35.8 + - + +
332B HIS* 3.4 14.9 - - - +
354B ARG* 3.8 24.9 - - - +
502B EDO 4.3 4.3 - - - +
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ARG* 4.9 0.7 + - - -
137B VAL 4.9 1.7 - - - +
139B LEU* 3.8 27.4 - - + +
142B ARG* 2.9 40.6 + - - -
310B ASP* 4.7 2.3 - - - +
311B ILE* 6.1 0.2 - - - +
313B LEU 4.4 8.2 - - - +
314B ILE* 3.7 39.6 - - + +
315B ILE 4.9 2.6 + - - +
316B THR* 5.6 1.6 - - - +
327B PRO* 3.0 3.3 + - + +
328B VAL* 1.3 81.6 - - - +
330B ILE* 1.3 62.7 + - - +
332B HIS* 2.9 22.7 + - + +
333B ILE* 3.0 24.8 + - + +
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Residues in contact with ILE 330 (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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190B LEU* 4.4 12.6 - - + -
232B PHE* 5.0 0.2 - - + -
234B TRP* 3.9 19.7 - - + +
259B ILE* 3.9 32.1 - - + -
288B CYS* 4.0 14.8 - - - -
314B ILE* 3.8 19.9 - - + +
327B PRO 3.1 18.1 + - - +
328B VAL 3.0 2.0 + - - +
329B GLU* 1.3 76.5 - - - +
331B PHE* 1.3 66.1 + - - +
333B ILE* 3.3 6.7 + - + +
334B ILE* 3.1 43.8 + - + +
502B EDO 3.3 32.1 - - - +
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 3.6 19.5 - - + -
328B VAL* 2.9 32.9 + - + +
330B ILE* 1.3 83.3 - - + +
332B HIS* 1.3 56.4 + - - +
334B ILE* 3.3 4.5 + - - +
335B GLU* 2.9 37.9 + - - +
345B HIS* 3.6 23.8 - + + -
352B THR* 4.0 19.1 - - - -
354B ARG* 3.5 35.4 - - - +
357B TRP* 3.5 40.4 - + + -
502B EDO 3.7 27.8 - - - -
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Residues in contact with HIS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.0 27.2 - - + +
153B ILE* 6.1 0.2 - - - +
157B ASP* 4.4 20.7 + - - -
310B ASP* 5.7 0.7 - - - +
328B VAL* 3.4 24.7 - - + +
329B GLU* 2.9 18.8 + - + +
331B PHE* 1.3 77.9 - - - +
333B ILE* 1.3 58.2 + - + +
335B GLU* 4.3 6.5 - - - -
336B HIS* 2.9 53.2 + - + -
354B ARG* 3.7 25.0 + - - -
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 4.1 32.8 - - + -
232B PHE* 5.3 2.9 - - + -
259B ILE* 4.3 18.6 - - + -
310B ASP* 3.8 27.8 - - + +
311B ILE 3.9 17.7 - - - +
313B LEU 4.7 0.4 - - - +
314B ILE* 3.9 35.0 - - + -
329B GLU* 3.0 19.7 + - + +
330B ILE* 3.7 8.7 - - + +
332B HIS* 1.3 77.8 - - + +
334B ILE* 1.3 64.1 + - + +
336B HIS* 3.9 1.7 - - - +
337B PHE* 3.1 23.4 + - + +
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Residues in contact with ILE 334 (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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188B VAL* 3.7 37.0 - - + -
190B LEU* 4.1 19.3 - - + -
232B PHE* 3.7 55.2 - - + -
330B ILE* 3.1 24.7 + - + +
331B PHE* 3.8 3.1 - - - +
333B ILE* 1.3 77.0 - - + +
335B GLU* 1.3 63.1 + - - +
337B PHE* 3.2 2.4 + - - +
338B CYS* 3.0 24.8 + - - +
343B ARG* 5.2 0.4 - - - -
357B TRP* 4.0 23.3 - - + -
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Residues in contact with GLU 335 (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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156B LYS* 4.6 2.1 + - - -
157B ASP* 5.4 1.4 - - - +
160B ILE* 3.6 45.6 - - + +
164B ASN* 5.3 1.0 + - - -
331B PHE* 2.9 21.7 + - - +
332B HIS* 4.1 5.0 - - - +
334B ILE* 1.3 76.7 - - - +
336B HIS* 1.3 60.9 + - - +
338B CYS 3.4 15.7 - - - +
339B LEU* 5.1 2.3 - - - +
343B ARG* 3.9 27.8 + - - +
354B ARG* 2.8 34.7 + - - -
355B PRO 4.5 3.1 - - - +
357B TRP* 2.8 30.3 + - + +
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Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 6.3 2.0 - - + -
153B ILE* 3.9 30.5 + - + +
156B LYS* 2.9 46.9 + - + +
157B ASP* 2.7 31.9 + - - -
160B ILE* 3.8 11.7 - - + -
306B HIS* 3.7 8.3 - - - +
309B VAL* 4.1 7.2 - - + -
310B ASP* 2.7 33.6 + - - +
332B HIS* 2.9 39.0 + - + +
333B ILE 3.9 0.4 - - - +
335B GLU* 1.3 78.3 - - - +
337B PHE* 1.3 63.9 + - - +
339B LEU* 4.4 1.4 - - - +
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Residues in contact with PHE 337 (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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475A TRP* 3.6 46.7 - + + -
476A LEU* 4.2 15.3 - - + -
230B PHE* 3.5 38.4 - + - -
232B PHE* 4.6 9.0 - + + -
290B MET* 3.4 29.6 - - + -
305B ILE* 3.1 25.9 - - + -
306B HIS 2.8 39.6 + - - +
307B ALA* 4.2 2.0 - - - -
309B VAL* 5.9 0.4 - - - -
333B ILE* 3.1 19.4 + - + +
334B ILE* 3.2 3.6 + - - +
336B HIS* 1.3 78.4 - - - +
338B CYS* 1.3 65.6 + - + +
339B LEU* 5.0 0.2 - - - -
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Residues in contact with CYS 338 (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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187B ASP* 4.2 2.9 - - - -
188B VAL* 3.6 33.2 - - + +
230B PHE* 4.4 3.8 - - + -
304B PHE* 3.5 37.7 - - - -
305B ILE* 4.5 0.2 - - - +
334B ILE 3.0 8.5 + - - +
335B GLU* 3.4 15.6 - - - +
337B PHE* 1.3 91.1 - - + +
339B LEU* 1.3 63.2 + - - +
340B GLY* 3.2 26.0 + - - +
343B ARG* 4.9 4.5 + - - -
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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