Contacts of the helix formed by residues 288 - 301 (chain B) in PDB entry 6IEH
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 ASN 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B ILE* 3.9 6.7 - - - +
287B PRO* 1.3 79.3 - - + +
289B ALA* 1.3 62.2 + - - -
290B ARG* 3.2 3.8 - - - -
291B GLN* 3.1 40.8 + - + +
292B PHE* 3.6 5.0 + - - +
558B PRO* 3.4 15.0 - - + +
559B LEU* 2.9 49.4 + - - +
560B ASN* 4.7 0.8 + - - -
589B PHE* 4.5 4.0 - - - -
593B GLN* 4.2 2.0 + - - -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 3.4 17.3 - - + +
160B SER* 4.5 8.3 - - - -
286B ILE* 3.5 35.9 + - + +
287B PRO 3.3 4.0 + - - -
288B ASN* 1.3 77.1 - - - +
290B ARG* 1.3 61.6 + - - +
292B PHE* 3.5 2.6 + - - +
293B ALA* 3.4 16.8 + - - +
306B VAL* 3.7 20.7 - - + +
308B TYR* 4.7 5.2 - - + -
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.6 28.8 - - + +
103B SER* 6.2 0.2 - - - -
113B GLU* 3.0 41.3 + - - +
115B ALA* 5.9 1.3 - - + -
287B PRO 5.2 0.8 + - - +
288B ASN* 3.2 1.5 - - - -
289B ALA* 1.3 77.2 - - - +
291B GLN* 1.3 63.4 + - - +
293B ALA* 3.1 4.0 + - - +
294B GLU* 3.1 37.6 + - + +
306B VAL* 3.9 14.2 - - + +
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ASN* 3.1 30.3 + - + +
290B ARG* 1.3 78.2 - - - +
292B PHE* 1.3 61.9 + - - +
294B GLU* 3.3 10.4 + - - +
295B TRP* 3.3 19.9 + - - +
589B PHE* 4.0 6.3 - - + -
592B PHE* 4.1 12.1 - - + -
593B GLN* 2.8 43.9 + - - +
596B ARG* 3.9 29.7 - - + +
597B ALA* 5.8 1.2 - - - +
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Residues in contact with PHE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 3.8 21.3 - - + -
254B ILE* 4.0 15.0 - - + -
257B MET* 3.9 28.9 - - + -
270B ILE* 4.4 0.7 - - + -
281B PHE* 3.6 47.8 - + + -
286B ILE* 5.6 1.8 - - + -
288B ASN* 3.6 6.6 + - - +
289B ALA* 3.5 8.9 + - - +
290B ARG 3.2 0.6 - - - -
291B GLN* 1.3 79.2 - - - +
293B ALA* 1.3 63.5 + - - +
295B TRP* 3.4 19.9 + + - +
296B ILE* 3.3 29.4 + - + +
559B LEU* 3.9 23.6 - - + -
589B PHE* 4.1 19.0 - + + -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ALA* 3.9 5.3 - - + +
158B LEU* 4.8 4.3 - - + -
289B ALA 3.4 3.6 + - - +
290B ARG 3.1 5.4 + - - +
292B PHE* 1.3 81.5 - - - +
294B GLU* 1.3 61.3 + - - +
296B ILE* 3.5 1.5 + - - -
297B CYS* 3.3 18.0 + - - +
304B CYS* 3.6 38.4 - - - +
305B HIS 4.9 0.2 - - - -
306B VAL* 3.4 34.1 - - + +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.8 15.0 - - + +
101B VAL* 3.3 32.7 - - + +
115B ALA* 4.1 9.2 - - + -
290B ARG* 3.1 28.3 + - - +
291B GLN* 3.7 9.2 - - - +
292B PHE 3.3 0.4 - - - -
293B ALA* 1.3 73.2 - - - +
295B TRP* 1.3 60.6 + - - +
297B CYS* 3.4 1.8 + - - +
298B HIS* 2.8 29.3 + - - +
592B PHE* 3.9 11.3 - - + -
596B ARG* 2.2 46.9 + - - -
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Residues in contact with TRP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B MET* 4.2 3.1 - - + -
267B GLU* 4.3 12.8 - - + -
270B ILE* 3.9 35.0 - - + -
271B ILE* 4.2 7.9 - - + -
291B GLN 3.3 7.4 + - - +
292B PHE* 3.7 34.8 - + - +
293B ALA 3.2 0.4 - - - -
294B GLU* 1.3 76.7 - - - +
296B ILE* 1.3 69.0 + - + +
298B HIS* 4.3 2.5 - + - -
299B LEU* 2.8 47.7 + - + +
587B LYS 3.2 25.5 + - - -
588B SER 3.6 5.2 + - - -
589B PHE* 3.7 48.0 - + + -
592B PHE* 3.8 34.2 - + + -
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Residues in contact with ILE 296 (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 SER* 5.3 1.1 - - - -
270B ILE* 4.2 17.0 - - + -
279B TYR* 4.2 15.0 - - + -
281B PHE* 3.3 32.8 - - + -
292B PHE* 3.3 30.9 + - + +
293B ALA 3.9 5.6 - - - +
294B GLU 3.3 0.6 - - - -
295B TRP* 1.3 84.9 - - + +
297B CYS* 1.3 62.1 + - - +
299B LEU* 4.5 3.4 - - - -
300B HIS* 2.7 43.3 + - + +
302B GLN* 4.6 5.7 - - + +
304B CYS* 4.0 21.5 - - + -
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Residues in contact with CYS 297 (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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99B VAL* 3.6 15.5 - - - -
115B ALA* 4.0 12.1 - - + +
116B LEU* 3.4 10.1 - - - -
117B PRO* 3.3 34.0 - - - +
293B ALA 3.3 10.9 + - - +
294B GLU 3.7 7.2 - - - +
295B TRP 3.2 0.2 - - - -
296B ILE* 1.3 81.3 - - - +
298B HIS* 1.3 58.4 + - - +
301B LYS* 2.7 28.4 + - - +
302B GLN 3.2 23.6 - - - +
304B CYS* 4.6 2.2 - - - +
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Residues in contact with HIS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 4.4 20.5 + - + +
99B VAL* 3.8 18.9 - - + +
294B GLU 2.8 19.0 + - - +
295B TRP* 3.8 5.6 - + - +
297B CYS* 1.3 78.1 - - - +
299B LEU* 1.3 61.6 + - + +
301B LYS* 2.6 40.4 + - - +
587B LYS* 5.0 7.5 + - + +
592B PHE* 3.9 28.3 - + + -
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Residues in contact with LEU 299 (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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270B ILE* 4.2 6.3 - - + +
271B ILE* 4.0 17.3 - - + +
275B ASP* 4.1 8.8 - - - +
295B TRP* 2.8 48.5 + - + +
296B ILE* 4.0 2.5 - - - +
298B HIS* 1.3 83.5 - - + +
300B HIS* 1.3 87.4 + - + +
301B LYS* 3.7 6.6 + - - +
583B TYR* 5.0 4.3 - - - +
587B LYS* 3.4 53.5 + - + +
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Residues in contact with HIS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.2 37.2 + - + +
271B ILE 5.1 1.2 + - - -
273B LEU 3.4 8.8 + - - -
274B PRO 3.9 8.5 - - - -
275B ASP* 3.2 40.2 - - - +
279B TYR* 3.2 40.0 + + - -
296B ILE* 2.7 27.5 + - - +
297B CYS 3.7 0.2 - - - -
299B LEU* 1.3 89.1 - - + +
301B LYS* 1.3 70.3 + - - +
302B GLN* 3.2 28.0 + - - +
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Residues in contact with LYS 301 (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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117B PRO* 3.9 16.0 - - + +
119B GLU* 5.5 6.7 - - - +
275B ASP* 4.3 10.3 - - + +
297B CYS 2.7 18.9 + - - -
298B HIS* 2.6 41.4 + - - +
299B LEU 3.5 8.9 + - - +
300B HIS* 1.3 72.8 - - - +
302B GLN* 1.3 57.4 + - - +
587B LYS* 4.8 12.9 - - - +
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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