Contacts of the helix formed by residues 54 - 64 (chain B) in PDB entry 4P22
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 LEU 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ARG* 3.3 42.4 - - + +
52B GLU* 3.2 8.6 + - - +
53B GLY* 1.3 78.0 - - - +
55B TYR* 1.3 66.2 + - - +
57B ARG* 3.3 6.0 - - + +
58B GLN* 3.1 15.9 + - - +
262B ASN* 3.6 29.4 - - - +
263B GLN* 3.2 35.4 - - + +
264B PRO 4.2 1.8 - - - -
265B MET* 4.0 14.4 - - + +
278B CYS* 4.0 26.2 - - + -
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Residues in contact with TYR 55 (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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385A LYS* 5.8 4.3 + - + -
429A LEU 5.3 2.3 + - - -
430A GLU 5.2 0.5 + - - -
54B LEU* 1.3 72.8 - - - +
56B SER* 1.3 68.7 + - - +
58B GLN* 3.2 12.9 + - - +
59B LEU* 3.2 34.6 + - + +
209B THR* 4.4 7.9 + - - -
247B PHE* 3.5 27.5 - + + -
263B GLN* 3.6 0.4 + - - +
264B PRO* 2.9 49.0 + - + +
295B VAL* 5.1 2.5 - - + -
296B LYS* 2.9 44.1 + - + +
417B PHE* 3.5 35.9 - + - -
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LYS* 4.0 18.6 - - - +
388A TYR* 4.5 4.8 - - - -
389A VAL* 3.6 8.1 - - - -
55B TYR* 1.3 83.6 - - - +
57B ARG* 1.3 57.7 + - - +
58B GLN 3.2 0.2 - - - -
59B LEU* 3.2 11.9 + - - +
60B TYR* 2.3 61.8 + - - -
263B GLN* 2.9 19.0 + - - +
264B PRO* 4.7 3.6 - - - +
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Residues in contact with ARG 57 (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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349A PRO* 4.2 10.4 - - + +
350A ARG* 3.3 53.4 - - + +
53B GLY* 4.6 5.7 - - - -
54B LEU* 3.3 16.2 - - + +
56B SER* 1.3 77.5 - - - +
58B GLN* 1.3 55.6 + - - +
60B TYR* 2.8 20.9 + - + +
61B VAL* 3.1 50.5 + - - +
65B GLU* 5.6 7.4 + - - +
69B ARG* 3.6 26.7 - - - +
263B GLN* 2.8 27.5 + - - +
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Residues in contact with GLN 58 (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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53B GLY* 3.1 32.3 + - - +
54B LEU 3.1 5.7 + - - -
55B TYR* 3.3 16.1 - - + +
56B SER 3.2 0.4 - - - -
57B ARG* 1.3 73.3 - - - +
59B LEU* 1.3 64.3 + - - +
61B VAL* 3.1 10.5 + - + +
62B LEU* 3.1 22.3 + - - +
247B PHE* 3.2 32.5 - - - -
266B GLU* 5.1 8.7 + - - +
417B PHE* 4.2 13.0 - - + -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.7 34.9 - - + +
385A LYS* 3.9 21.1 - - - +
429A LEU* 3.0 37.4 - - + +
55B TYR* 3.2 26.9 + - + +
56B SER* 3.2 21.5 + - - +
58B GLN* 1.3 76.2 - - - +
60B TYR* 1.3 63.5 + - + +
62B LEU* 3.4 4.0 + - - +
63B GLY* 3.1 18.0 + - - -
417B PHE* 3.0 37.9 - - + -
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.8 10.8 - - + -
349A PRO* 4.0 8.7 - - + -
388A TYR* 3.0 28.7 + - - +
389A VAL* 2.3 60.1 - - + +
392A GLY* 6.1 3.4 - - - -
394A LEU* 4.4 5.0 - - + +
56B SER* 2.3 36.7 - - - -
57B ARG* 2.8 41.0 + - + +
58B GLN 3.2 0.2 - - - -
59B LEU* 1.3 77.0 - - + +
61B VAL* 1.3 60.7 + - - +
63B GLY* 3.0 9.3 + - - -
64B HIS 3.2 0.3 + - - -
65B GLU* 3.0 48.0 + - + +
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Residues in contact with VAL 61 (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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57B ARG* 3.1 40.8 + - - +
58B GLN* 3.1 12.0 + - + +
60B TYR* 1.3 72.8 - - + +
62B LEU* 1.3 65.8 + - - +
64B HIS* 3.2 12.1 + - - -
65B GLU* 4.3 6.9 + - + +
66B ALA* 4.7 10.5 - - + +
69B ARG* 3.1 46.4 - - - +
71B GLN* 6.0 0.2 + - - -
414B SER* 5.5 5.7 - - - +
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Residues in contact with LEU 62 (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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429A LEU* 3.9 11.9 - - + -
58B GLN 3.1 11.7 + - - +
59B LEU 3.6 6.7 - - - +
61B VAL* 1.3 77.9 - - - +
63B GLY* 1.3 63.4 + - - +
64B HIS* 3.2 1.2 + - - -
410B MET* 2.9 53.4 - - + +
411B LYS* 3.9 21.1 - - + -
414B SER* 3.3 37.5 - - - +
415B GLY* 3.5 1.1 - - - +
417B PHE* 2.8 39.5 - - + -
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Residues in contact with GLY 63 (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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194A LEU* 6.3 0.2 - - - -
394A LEU* 4.3 14.3 - - - +
396A PRO* 4.0 7.7 - - - +
59B LEU 3.1 10.8 + - - -
60B TYR 3.0 8.9 + - - -
62B LEU* 1.3 78.1 - - - +
64B HIS* 1.3 86.5 + - - +
65B GLU 3.5 0.7 - - - -
410B MET* 4.3 7.9 - - - +
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Residues in contact with HIS 64 (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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113A SER* 3.5 23.8 - - - -
393A ASP 3.5 7.9 - - - -
394A LEU* 2.7 15.8 - - + -
395A ALA* 2.5 38.9 + - + -
396A PRO* 3.4 9.6 - - + -
61B VAL 3.2 7.8 + - - -
62B LEU 3.1 5.8 - - - -
63B GLY* 1.3 97.3 - - - +
65B GLU* 1.3 67.1 + - - +
66B ALA 3.2 8.8 + - - -
67B MET* 3.7 12.5 - - - +
93B LEU 3.2 19.0 + - - -
94B GLY* 2.7 35.0 - - - +
410B MET* 4.3 3.8 - - + -
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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