Contacts of the helix formed by residues 347 - 364 (chain B) in PDB entry 2H3W
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 GLU 347 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TRP* 4.8 2.4 + - - -
107B TYR* 4.6 2.4 + - - -
172B GLN* 2.7 31.4 + - - +
341B TYR* 3.6 5.4 - - - -
343B HIS* 3.2 14.1 - - - -
346B ALA* 1.3 73.2 - - - +
348B GLY* 1.3 67.4 + - - +
349B PRO* 3.7 11.0 - - + -
350B PRO* 3.5 7.6 - - + +
351B ILE* 3.1 21.0 + - - +
458B ARG* 6.2 0.7 - - + -
464B ARG* 2.8 40.6 + - - +
465B THR* 3.5 21.3 - - + +
1701B COA 3.1 27.9 - - + +
1702B HC5 3.4 9.3 - - - +
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Residues in contact with GLY 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B TYR* 3.5 10.7 + - - -
347B GLU* 1.3 74.9 - - - +
349B PRO* 1.3 70.7 - - - +
351B ILE* 2.8 8.8 + - - +
352B VAL* 2.8 30.6 + - - +
556B VAL* 5.0 1.3 - - - -
1701B COA 3.2 18.5 - - - -
1702B HC5 4.0 12.3 - - - -
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Residues in contact with PRO 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU* 6.0 0.2 - - - -
173B TYR* 4.7 1.8 - - - -
347B GLU* 3.8 2.9 - - + -
348B GLY* 1.3 86.6 - - - +
350B PRO* 1.3 71.4 - - + +
352B VAL* 2.9 16.3 - - + +
353B ALA* 2.9 23.4 + - - +
456B SER* 5.4 3.6 - - - +
458B ARG* 4.1 15.7 - - - +
555B GLN 5.5 1.6 - - - +
556B VAL* 5.4 1.5 - - + -
557B PRO* 5.6 9.0 - - + -
1701B COA 3.4 45.3 - - - +
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Residues in contact with PRO 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN* 3.1 46.4 - - + +
173B TYR* 3.5 31.9 - - + +
176B ILE* 5.1 4.6 - - + +
346B ALA* 4.4 5.4 - - + -
347B GLU* 3.5 13.7 - - + +
349B PRO* 1.3 99.8 - - + +
351B ILE* 1.3 61.4 + - + +
353B ALA* 3.3 9.7 + - - +
354B LEU* 3.4 12.1 + - - +
458B ARG* 4.0 17.2 - - - +
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Residues in contact with ILE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 5.1 5.2 - - + -
176B ILE* 3.8 25.4 - - + -
326B THR* 5.8 0.2 - - + -
327B LEU* 3.7 26.9 - - + -
339B MET* 3.5 31.4 - - + -
341B TYR* 4.0 32.1 - - + -
346B ALA* 5.0 1.6 - - + -
347B GLU 3.1 17.9 - - - +
348B GLY* 2.8 14.2 + - - +
350B PRO* 1.3 73.6 - - + +
352B VAL* 1.3 59.0 + - + +
354B LEU* 3.2 9.9 + - + +
355B VAL* 2.9 27.0 + - + +
1702B HC5 5.7 0.7 - - + -
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLY* 2.8 19.7 + - - +
349B PRO* 2.9 21.8 - - + +
351B ILE* 1.3 71.2 - - + +
353B ALA* 1.3 63.8 + - + +
355B VAL* 3.6 9.1 - - - +
356B ASP* 2.8 37.4 + - - +
556B VAL* 3.2 34.3 - - + -
557B PRO* 3.6 18.8 - - + +
558B ALA* 4.1 15.7 - - + -
1702B HC5 5.6 1.6 - - + -
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Residues in contact with ALA 353 (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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149B PHE* 4.1 8.0 - - + -
161B GLU* 4.0 9.6 - - - +
173B TYR* 3.4 29.8 - - + +
349B PRO 2.9 10.0 + - - +
350B PRO 3.5 5.8 - - - +
352B VAL* 1.3 80.7 - - + +
354B LEU* 1.3 63.3 + - - +
356B ASP* 3.5 7.1 + - - +
357B HIS* 3.1 22.9 + - - +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 4.6 7.6 - - + -
149B PHE* 3.8 37.0 - - + -
176B ILE* 3.6 27.1 - - + -
177B LEU* 4.5 9.0 - - + -
327B LEU* 4.2 14.6 - - + -
329B PHE* 3.5 33.4 - - + -
339B MET* 5.6 0.9 - - + -
350B PRO 3.4 8.1 + - - +
351B ILE* 3.2 12.9 + - + +
353B ALA* 1.3 77.5 - - - +
355B VAL* 1.3 62.6 + - + +
357B HIS* 3.2 2.3 + - - +
358B VAL* 2.8 46.6 + - + +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 5.2 4.3 - - + -
124B LEU* 3.3 32.3 - - + -
329B PHE* 4.9 4.3 - - + -
339B MET* 3.4 31.9 - - + -
351B ILE* 2.9 21.5 + - + +
352B VAL* 3.2 11.4 + - - +
354B LEU* 1.3 82.0 - - + +
356B ASP* 1.3 58.7 + - - +
358B VAL* 3.2 4.1 + - - +
359B MET* 2.8 40.4 + - + +
560B THR* 4.2 9.6 - - - +
562B CYS* 4.8 6.3 - - - -
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Residues in contact with ASP 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B VAL* 2.8 26.9 + - - +
353B ALA* 3.8 7.0 - - - +
355B VAL* 1.3 73.5 - - - +
357B HIS* 1.3 61.1 + - - +
359B MET* 4.1 0.9 - - - +
360B GLU* 3.1 26.5 + - - +
558B ALA* 3.6 10.9 - - - +
559B LYS* 2.9 53.9 + - + +
560B THR* 2.5 44.4 + - - -
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Residues in contact with HIS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLY 3.8 4.6 + - - -
148B ASP* 2.8 35.0 + - + -
149B PHE* 3.6 29.8 - + + +
152B MET* 3.5 27.5 - - + +
353B ALA 3.1 15.2 + - - +
354B LEU 3.4 7.2 - - - +
356B ASP* 1.3 74.3 - - - +
358B VAL* 1.3 66.9 + - - +
360B GLU* 3.3 12.8 + - - +
361B TYR* 3.0 26.7 + + - +
364B LYS* 4.9 9.9 + - - -
559B LYS* 5.9 1.1 - - - +
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.7 35.4 - - + +
145B GLY* 3.8 5.6 - - - +
146B VAL* 3.6 35.0 - - + +
149B PHE* 5.2 0.4 - - + -
329B PHE* 5.0 2.9 - - + -
354B LEU* 2.8 36.7 + - + +
355B VAL* 3.8 4.0 - - - +
357B HIS* 1.3 73.9 - - + +
359B MET* 1.3 82.3 + - + +
361B TYR* 3.0 9.0 + - - +
362B THR* 3.0 25.9 + - + +
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Residues in contact with MET 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.7 33.0 - - + -
125B PRO* 5.1 2.2 - - + -
127B GLN* 5.0 7.6 - - - -
138B PHE* 4.5 15.5 - - + -
142B LEU* 4.2 15.3 - - + -
329B PHE* 5.5 3.1 - - + -
355B VAL* 2.8 30.4 + - + +
356B ASP 4.1 0.4 - - - +
358B VAL* 1.3 102.8 - - + +
360B GLU* 1.3 61.5 + - - +
362B THR* 2.6 26.8 + - + -
363B LYS* 3.4 22.9 + - - +
560B THR* 3.8 34.1 - - + +
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Residues in contact with GLU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ASP 3.1 20.6 + - - +
357B HIS* 3.7 11.2 - - - +
359B MET* 1.3 77.1 - - - +
361B TYR* 1.3 57.5 + - - +
363B LYS* 3.1 16.4 + - + +
364B LYS* 3.0 44.5 + - + +
559B LYS* 4.9 12.8 + - - -
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Residues in contact with TYR 361 (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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141B LYS* 3.6 17.2 + - + -
144B GLU* 3.0 53.6 + - + +
145B GLY* 3.6 20.9 - - - -
148B ASP* 3.9 37.4 - - + +
357B HIS* 3.0 16.0 + + + +
358B VAL 3.0 9.4 + - - +
360B GLU* 1.3 73.1 - - - +
362B THR* 1.3 63.2 + - - +
363B LYS 2.9 5.4 - - - -
364B LYS* 3.0 45.2 + - + +
368B VAL* 5.5 6.2 - - - +
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Residues in contact with THR 362 (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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127B GLN* 5.0 2.8 + - - -
138B PHE* 4.0 33.3 - - + -
141B LYS* 3.1 33.9 + - + +
142B LEU* 4.0 28.3 - - + +
358B VAL* 3.0 17.8 + - + +
359B MET* 2.6 24.7 + - + -
361B TYR* 1.3 75.0 - - - +
363B LYS* 1.3 63.4 + - - +
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Residues in contact with LYS 363 (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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125B PRO* 5.7 7.7 - - - +
127B GLN* 5.4 8.9 + - - +
359B MET* 3.4 27.1 + - - +
360B GLU* 3.1 17.4 + - + +
361B TYR 2.9 0.4 - - - -
362B THR* 1.3 84.4 + - - +
364B LYS* 1.3 63.9 + - - +
365B PRO* 3.5 5.0 - - - +
560B THR* 6.0 1.2 - - - +
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 2.9 25.3 + - - -
148B ASP* 4.6 8.5 + - - -
357B HIS* 4.9 8.5 + - - -
360B GLU* 3.0 35.7 + - + +
361B TYR* 3.0 44.8 + - + +
363B LYS* 1.3 77.1 - - - +
365B PRO* 1.3 73.9 - - + +
366B GLU* 3.5 0.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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