Contacts of the helix formed by residues 347 - 363 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TRP* 4.8 1.7 + - - -
107A TYR* 4.3 2.8 + - - -
172A GLN* 2.7 29.2 + - - +
341A TYR* 3.5 6.1 - - - -
343A HIS* 3.2 10.5 - - - -
346A ALA* 1.3 72.4 - - - +
348A GLY* 1.3 65.2 + - - +
349A PRO* 3.8 10.1 - - + -
350A PRO* 3.7 5.3 - - + +
351A ILE* 3.0 26.0 + - - +
458A ARG* 6.1 0.4 - - - -
464A ARG* 2.6 45.9 + - - +
465A THR* 3.5 24.5 - - + +
1601A COA 3.0 28.4 - - + +
1602A HC5 3.3 8.5 - - - +
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Residues in contact with GLY 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.9 8.3 - - - -
347A GLU* 1.3 76.4 - - - +
349A PRO* 1.3 71.9 - - - +
351A ILE* 2.9 9.2 + - - +
352A VAL* 2.9 28.3 + - - +
556A VAL* 5.2 1.6 - - - -
1601A COA 3.3 19.1 - - - -
1602A HC5 4.1 12.3 - - - -
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Residues in contact with PRO 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 5.8 1.1 - - - +
173A TYR* 4.6 1.3 - - - -
347A GLU* 3.9 3.1 - - + -
348A GLY* 1.3 86.0 - - - +
350A PRO* 1.3 65.8 - - + +
352A VAL* 2.9 14.4 - - + +
353A ALA* 2.8 31.7 + - - +
456A SER* 5.3 4.7 - - - +
458A ARG* 3.9 17.3 - - - +
556A VAL* 6.2 1.5 - - + -
557A PRO* 5.6 8.3 - - + -
1601A COA 3.4 44.0 - - + +
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Residues in contact with PRO 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLN* 3.0 47.1 - - + +
173A TYR* 3.6 35.0 - - + +
176A ILE* 5.1 4.8 - - + +
346A ALA* 4.4 6.3 - - + -
347A GLU* 3.7 6.1 - - + +
348A GLY 3.5 4.0 - - - -
349A PRO* 1.3 99.0 - - + +
351A ILE* 1.3 61.8 + - - +
353A ALA* 3.2 3.6 + - - +
354A LEU* 3.1 20.6 + - - +
458A ARG* 4.2 16.4 - - - +
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Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 4.9 7.2 - - + -
176A ILE* 4.0 22.2 - - + -
326A THR* 6.0 0.4 - - + -
327A LEU* 3.7 27.6 - - + -
339A MET* 3.4 30.7 - - + -
341A TYR* 3.8 33.9 - - + -
346A ALA* 4.9 1.8 - - + -
347A GLU 3.0 18.6 + - - +
348A GLY* 2.9 8.6 + - - +
350A PRO* 1.3 75.6 - - - +
352A VAL* 1.3 61.6 + - + +
354A LEU* 3.1 11.8 + - + +
355A VAL* 3.0 25.5 + - + +
1602A HC5 5.4 0.9 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 5.9 5.4 - - + -
348A GLY* 2.9 17.3 + - - +
349A PRO* 2.9 33.9 - - + +
351A ILE* 1.3 76.4 - - + +
353A ALA* 1.3 60.3 + - - +
355A VAL* 3.4 10.6 - - + +
356A ASP* 2.8 35.8 + - - +
556A VAL* 4.6 19.3 - - + -
557A PRO* 3.4 26.2 - - + +
558A ALA* 4.1 14.6 - - + -
562A CYS* 5.3 6.5 - - - -
1602A HC5 5.3 6.1 - - + -
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 4.2 5.9 - - + -
161A GLU* 4.7 7.9 - - - +
173A TYR* 3.2 30.1 - - + +
349A PRO 2.8 13.9 + - - +
350A PRO 3.4 3.1 - - - +
352A VAL* 1.3 78.1 - - + +
354A LEU* 1.3 62.9 + - - +
356A ASP* 3.5 8.0 + - - +
357A HIS* 3.2 22.7 + - - +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A VAL* 4.8 7.0 - - + -
149A PHE* 3.9 35.3 - - + -
176A ILE* 3.7 26.2 - - + -
177A LEU* 4.7 8.5 - - + -
327A LEU* 4.2 17.9 - - + -
329A PHE* 3.4 31.9 - - + -
339A MET* 5.4 1.1 - - - -
350A PRO 3.1 12.1 + - - +
351A ILE* 3.4 11.9 - - + +
353A ALA* 1.3 78.4 - - - +
355A VAL* 1.3 60.8 + - + +
357A HIS* 3.4 2.1 + - - +
358A VAL* 2.9 46.2 + - + +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 5.2 4.3 - - + -
124A LEU* 3.5 32.8 - - + -
329A PHE* 4.9 4.0 - - + -
339A MET* 3.7 29.2 - - + -
351A ILE* 3.0 18.8 + - + +
352A VAL* 3.4 13.7 - - + +
354A LEU* 1.3 80.1 - - + +
356A ASP* 1.3 64.2 + - - +
358A VAL* 3.1 4.6 + - - +
359A MET* 2.8 41.9 + - + +
560A THR* 3.9 12.1 - - - +
562A CYS* 4.8 5.8 - - - -
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A VAL* 2.8 25.2 + - - +
353A ALA* 3.8 7.5 - - - +
355A VAL* 1.3 71.2 - - - +
357A HIS* 1.3 58.7 + - - +
359A MET* 4.1 0.7 - - - +
360A GLU* 3.1 30.7 + - - +
558A ALA* 3.7 10.9 - - - +
559A LYS* 2.9 53.3 + - + +
560A THR* 2.6 40.8 + - - +
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Residues in contact with HIS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY 3.8 8.1 + - - -
148A ASP* 2.9 30.3 + - + -
149A PHE* 3.6 39.1 - + + +
152A MET* 3.5 23.0 - - + +
353A ALA 3.2 14.3 + - - +
354A LEU 3.6 4.0 - - - +
355A VAL 3.1 0.4 - - - -
356A ASP* 1.3 77.5 - - - +
358A VAL* 1.3 66.0 + - - +
360A GLU* 3.4 5.4 + - - +
361A TYR* 3.0 26.3 + + - +
364A LYS* 6.1 0.8 + - - -
559A LYS* 6.0 0.9 - - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.7 35.2 - - + +
145A GLY* 3.9 6.3 - - - +
146A VAL* 3.8 26.0 - - + +
149A PHE* 5.1 0.7 - - + -
329A PHE* 5.1 3.6 - - + -
354A LEU* 2.9 40.9 + - + +
355A VAL* 3.7 4.9 - - - +
357A HIS* 1.3 79.3 - - - +
359A MET* 1.3 80.9 + - + +
361A TYR* 2.9 17.8 + - - +
362A THR* 3.0 17.7 + - - +
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Residues in contact with MET 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.0 30.3 - - + -
125A PRO* 5.0 2.0 - - - -
127A GLN* 4.8 9.0 - - - -
138A PHE* 4.0 27.4 - - + -
142A LEU* 4.4 6.3 - - + -
329A PHE* 6.0 1.6 - - + -
337A CYS* 5.1 0.2 - - - -
355A VAL* 2.8 38.5 + - + +
358A VAL* 1.3 91.3 - - + +
360A GLU* 1.3 62.3 + - - +
362A THR* 2.6 26.8 + - + -
363A LYS* 3.3 26.8 + - - +
560A THR* 3.8 23.6 - - + +
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Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASP 3.1 20.9 + - - +
357A HIS* 3.8 5.6 - - - +
359A MET* 1.3 77.3 - - - +
361A TYR* 1.3 60.6 + - - +
363A LYS* 3.4 27.8 + - - +
364A LYS* 3.6 24.9 + - - +
559A LYS* 5.6 8.5 + - - +
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Residues in contact with TYR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS* 3.5 21.4 - - + -
144A GLU* 2.9 51.7 + - + +
145A GLY* 3.5 22.0 - - - -
148A ASP* 3.8 34.6 + - + +
357A HIS* 3.0 16.8 + + + +
358A VAL 2.9 12.7 + - - +
360A GLU* 1.3 75.1 - - - +
362A THR* 1.3 56.0 + - - +
363A LYS 3.0 5.2 - - - -
364A LYS* 3.0 49.0 + - + +
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Residues in contact with THR 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN* 4.6 3.0 + - - -
138A PHE* 3.8 33.7 - - + -
141A LYS* 3.0 31.7 + - + +
142A LEU* 4.0 28.0 - - - +
358A VAL 3.0 16.5 + - - +
359A MET* 2.6 26.5 + - + +
361A TYR* 1.3 76.0 - - - +
363A LYS* 1.3 63.2 + - - +
364A LYS 3.4 0.2 - - - -
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PRO* 6.1 3.2 - - - +
127A GLN* 5.7 5.7 + - - +
141A LYS* 4.6 0.2 - - - -
359A MET* 3.3 33.1 + - - +
360A GLU* 3.7 27.8 - - - +
361A TYR 3.0 1.4 - - - -
362A THR* 1.3 81.5 + - - +
364A LYS* 1.3 64.7 + - - +
365A PRO* 3.6 4.7 - - - +
560A THR* 6.0 1.4 - - - +
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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