Contacts of the helix formed by residues 71 - 78 (chain C) in PDB entry 4K9P
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 SER 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASN* 4.0 5.6 - - - -
28C GLU* 3.5 1.8 + - - -
69C LEU 3.5 3.4 + - - -
70C HIS* 1.3 88.2 - - - +
72C ALA* 1.3 63.0 + - - +
73C ALA 4.6 1.1 - - - -
75C THR* 2.7 32.6 + - - -
96C ALA* 4.0 2.5 - - - +
97C GLY 3.1 27.9 + - - +
110C LEU* 2.6 33.3 + - - -
111C THR 4.1 0.3 - - - -
112C ASN* 3.5 20.9 + - - +
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A MET 5.2 0.2 - - - +
80A GLY* 4.9 0.5 - - - -
83A SER* 4.7 15.2 - - - +
122A LEU* 5.3 8.0 - - + +
71C SER* 1.3 83.7 + - - +
73C ALA* 1.3 55.3 + - - +
75C THR* 3.7 0.5 - - - -
76C GLY* 2.7 33.3 + - - -
111C THR 4.8 3.6 - - - +
112C ASN* 3.3 32.2 - - - +
113C VAL 5.2 0.7 - - - +
118C LEU* 3.8 12.5 - - + +
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Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 3.6 7.8 - - - +
83A SER* 3.9 16.1 + - - +
400A ALA* 5.0 3.6 - - + +
401A GLY 4.9 1.1 - - - +
402A GLY* 3.5 33.4 - - - +
602A TPP 4.1 13.7 - - + +
70C HIS* 3.7 4.9 + - + +
71C SER* 3.5 1.4 - - - -
72C ALA* 1.3 78.8 - - - +
74C GLY* 1.3 57.3 + - - +
77C ASN* 3.0 34.7 + - - -
110C LEU* 6.5 0.7 - - + -
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Residues in contact with GLY 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A TPP 4.2 2.3 - - - +
47C GLU* 3.1 44.0 - - - +
69C LEU* 3.9 5.1 - - - +
70C HIS* 2.8 24.9 + - - -
73C ALA* 1.3 75.5 - - - +
75C THR* 1.3 65.1 + - - +
77C ASN 3.2 6.6 + - - -
78C ALA* 3.5 5.4 + - - +
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Residues in contact with THR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 4.0 13.6 - - + +
71C SER 2.7 24.3 + - - -
72C ALA 3.7 3.4 - - - -
74C GLY* 1.3 73.7 - - - +
76C GLY* 1.3 64.9 + - - +
78C ALA* 2.9 17.0 + - + +
79C MET* 3.5 19.0 + - - +
82C LEU* 5.5 3.5 - - + +
94C VAL* 5.7 0.4 - - + -
96C ALA* 3.5 6.1 - - - +
118C LEU* 3.8 22.7 - - + -
119C PRO* 4.8 3.6 - - + -
155C TYR* 2.8 41.0 + - + -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLY 3.1 21.8 - - - +
79A MET* 3.3 15.7 - - - +
80A GLY 3.3 17.8 + - - -
72C ALA 2.7 21.9 + - - -
73C ALA 3.8 0.2 - - - -
75C THR* 1.3 75.2 - - - +
77C ASN* 1.3 61.6 + - - +
78C ALA 2.9 1.4 + - - -
79C MET* 3.2 7.6 + - - +
118C LEU* 4.4 6.2 - - - +
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Residues in contact with ASN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLN* 5.5 1.2 + - - -
48A ALA* 4.7 6.8 - - - +
76A GLY 4.8 0.7 - - - -
77A ASN* 4.4 21.5 - - - +
80A GLY* 3.3 20.1 + - - +
81A ALA 4.2 1.7 + - - -
403A LEU 4.1 9.4 + - - +
433A TYR* 4.2 1.8 - - - +
602A TPP 3.2 23.8 - - - +
46C GLN* 3.7 21.6 + - - +
47C GLU* 3.1 35.8 + - + +
48C ALA* 3.8 18.4 - - - +
73C ALA 3.0 14.0 + - - +
74C GLY 3.2 0.6 + - - -
76C GLY* 1.3 74.4 - - - +
78C ALA* 1.3 58.1 + - - +
79C MET 3.5 0.6 + - - -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU* 4.0 7.9 - - + +
48C ALA* 4.3 8.1 - - - +
51C VAL* 3.7 26.7 - - + -
69C LEU* 3.8 10.8 - - + -
74C GLY 3.7 9.0 - - - +
75C THR 2.9 9.6 + - - +
76C GLY 2.9 1.6 + - - -
77C ASN* 1.3 79.2 - - - +
79C MET* 1.3 58.4 + - - +
80C GLY 3.4 2.5 - - - -
81C ALA* 3.2 9.4 + - - +
82C LEU* 3.0 29.0 + - + +
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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