Contacts of the helix formed by residues 386 - 400 (chain A) in PDB entry 4H36
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 THR 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLN* 4.7 3.8 - - - +
385A HIS* 1.3 73.1 - - - +
387A ILE* 1.3 59.2 + - - +
388A GLU* 3.8 6.5 + - - +
389A GLU* 3.0 40.0 + - - +
390A TRP* 2.8 32.6 + - - -
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Residues in contact with ILE 387 (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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99A PHE* 3.7 37.4 - - + +
100A GLN 4.0 4.5 - - - +
101A ASN* 3.6 13.7 - - - -
102A GLN* 3.5 38.2 - - + +
105A ALA* 4.7 2.9 - - + +
386A THR* 1.3 73.1 - - - +
388A GLU* 1.3 59.2 + - - +
390A TRP* 3.4 9.6 + - - +
391A LYS* 2.8 31.6 + - - +
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR* 3.2 6.5 + - - +
387A ILE* 1.3 78.6 - - - +
389A GLU* 1.3 65.6 - - + +
391A LYS* 3.2 24.5 + - + +
392A GLU* 3.2 29.8 + - + +
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Residues in contact with GLU 389 (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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385A HIS* 3.4 27.3 + - + +
386A THR* 3.0 40.4 + - - +
388A GLU* 1.3 76.6 - - + +
390A TRP* 1.3 66.8 + - - +
392A GLU* 3.2 20.7 + - - +
393A LEU* 3.3 18.4 + - + +
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Residues in contact with TRP 390 (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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102A GLN* 4.1 15.6 + - + +
105A ALA* 3.5 28.7 - - + +
106A LYS* 3.7 38.9 - - + +
109A TYR* 3.4 44.9 - + + -
380A LEU* 4.3 16.6 - - + -
383A ARG* 4.1 8.3 - - + -
384A GLU* 4.3 1.2 + - - +
385A HIS* 3.0 48.4 + + + +
386A THR 2.8 27.7 + - - +
387A ILE 3.5 5.4 - - - +
389A GLU* 1.3 76.7 - - - +
391A LYS* 1.3 63.0 + - - +
392A GLU 3.2 0.2 + - - -
393A LEU* 3.3 20.2 + - + +
394A ILE* 3.1 29.0 + - - +
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Residues in contact with LYS 391 (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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99A PHE* 3.6 45.1 - - + +
136A LEU* 4.0 18.8 - - + +
137A GLU 4.5 11.1 + - - -
139A PHE* 3.2 42.4 + - + +
140A GLN* 5.5 1.4 - - - +
387A ILE* 2.8 18.6 + - - +
388A GLU* 3.2 21.2 + - + +
390A TRP* 1.3 75.5 - - - +
392A GLU* 1.3 56.0 + - - +
394A ILE* 3.7 0.7 - - - +
395A TYR* 3.0 21.5 + - - +
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Residues in contact with GLU 392 (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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136A LEU* 3.7 32.5 - - + +
388A GLU* 3.2 31.0 + - + +
389A GLU* 3.6 11.0 - - - +
390A TRP 3.1 0.8 - - - -
391A LYS* 1.3 72.9 - - + +
393A LEU* 1.3 57.2 + - + +
394A ILE 3.1 1.3 - - - -
395A TYR* 2.8 8.6 + - - +
396A LYS* 2.8 35.8 + - - +
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Residues in contact with LEU 393 (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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109A TYR* 3.6 28.8 - - + +
385A HIS* 3.8 36.8 - - + +
389A GLU 3.3 11.9 + - - +
390A TRP* 3.3 23.9 + - + +
392A GLU* 1.3 78.3 - - + +
394A ILE* 1.3 60.5 + - - +
396A LYS* 3.8 5.8 + - - +
397A GLU* 3.3 26.9 + - - +
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Residues in contact with ILE 394 (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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95A LEU* 6.4 0.2 - - + -
98A PRO* 5.4 0.2 - - + -
99A PHE* 3.5 25.6 - - + -
105A ALA 3.6 22.2 - - - +
108A ALA* 3.8 10.3 - - + +
109A TYR* 3.5 30.7 - - + +
112A LEU* 3.8 17.9 - - + -
139A PHE* 4.0 17.9 - - + -
142A VAL* 4.1 13.7 - - + -
390A TRP 3.1 16.7 + - - +
391A LYS 3.7 4.3 - - - +
393A LEU* 1.3 74.8 - - - +
395A TYR* 1.3 65.6 + - - +
397A GLU* 3.1 6.9 + - - +
398A VAL* 3.0 22.4 + - + +
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Residues in contact with TYR 395 (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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131A THR* 4.3 15.0 - - + -
133A GLN 4.9 1.8 - - - -
134A LYS 3.3 24.1 + - - -
135A THR* 3.6 7.7 - - - -
136A LEU* 3.8 35.0 - - + -
139A PHE* 3.3 47.1 - + + -
391A LYS 3.0 18.9 + - - +
392A GLU* 2.8 11.7 + - - +
394A ILE* 1.3 72.4 - - - +
396A LYS* 1.3 62.7 + - - +
398A VAL* 3.2 6.1 + - + +
399A MET* 3.0 49.5 + - + +
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Residues in contact with LYS 396 (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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392A GLU 2.8 17.7 + - - +
393A LEU* 4.1 6.5 - - + +
395A TYR* 1.3 76.4 - - - +
397A GLU* 1.3 57.2 + - + +
399A MET* 3.3 6.7 + - - +
400A ASN* 2.9 29.3 + - - +
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Residues in contact with GLU 397 (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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109A TYR* 4.0 20.3 + - + -
112A LEU* 4.1 23.0 - - + +
113A VAL* 5.3 5.2 - - + +
116A LYS* 3.8 30.3 - - - +
129A VAL* 4.6 7.1 - - - +
393A LEU 3.3 15.3 + - - +
394A ILE 3.1 10.2 + - - +
396A LYS* 1.3 78.8 - - + +
398A VAL* 1.3 62.8 + - - +
400A ASN* 3.3 31.2 + - - +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.5 3.1 - - + -
129A VAL* 4.0 33.8 - - + +
130A PHE* 3.8 22.4 - - - -
131A THR* 3.7 27.8 - - + +
139A PHE* 4.9 3.8 - - + -
142A VAL* 4.4 18.4 - - + -
394A ILE* 3.0 25.3 + - + +
395A TYR* 3.2 10.1 + - - +
397A GLU* 1.3 79.4 - - - +
399A MET* 1.3 68.6 + - - +
400A ASN 3.2 6.2 + - - +
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Residues in contact with MET 399 (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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131A THR* 4.4 13.9 - - + +
133A GLN 4.6 6.7 - - - +
134A LYS* 5.1 3.4 - - - +
395A TYR* 3.0 53.8 + - + +
396A LYS* 3.9 6.3 - - - +
398A VAL* 1.3 89.7 - - - +
400A ASN* 1.3 64.5 + - - +
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Residues in contact with ASN 400 (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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116A LYS* 5.6 5.5 - - - +
129A VAL* 5.7 2.4 - - - +
396A LYS 2.9 12.8 + - - +
397A GLU* 3.3 31.8 + - - +
398A VAL 3.1 7.6 - - - +
399A MET* 1.3 83.5 - - - +
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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