Contacts of the helix formed by residues 71 - 78 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ASN* 3.8 9.3 + - - -
28B GLU* 3.3 1.6 + - - -
69B LEU 4.0 1.6 + - - -
70B HIS* 1.3 94.7 - - - +
72B ALA* 1.3 65.4 + - - +
73B ALA* 4.4 3.8 - - - -
75B THR* 3.1 21.5 + - - -
96B ALA* 4.1 2.3 - - - +
97B GLY 3.2 23.6 + - - +
110B LEU* 2.5 36.0 + - - -
111B THR 3.9 0.9 + - - -
112B ASN* 3.8 18.6 + - - +
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Residues in contact with ALA 72 (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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71B SER* 1.3 79.3 + - - +
73B ALA* 1.3 55.4 + - - +
75B THR* 3.8 0.2 - - - -
76B GLY* 2.6 34.3 + - - -
111B THR 4.9 3.1 - - - +
112B ASN* 3.2 31.1 - - + +
113B VAL 5.4 0.4 - - - +
118B LEU* 3.7 19.9 - - + +
80D GLY* 5.0 0.5 - - - -
83D SER* 4.9 14.0 - - - -
122D LEU* 5.2 9.9 - - + +
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Residues in contact with ALA 73 (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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70B HIS* 4.4 5.8 - - + +
71B SER* 3.3 2.3 - - - -
72B ALA* 1.3 79.5 - - - +
74B GLY* 1.3 62.7 + - - +
77B ASN* 3.0 27.4 + - - -
110B LEU* 6.4 1.1 - - + -
80D GLY* 3.7 9.7 - - - +
83D SER* 4.3 14.8 + - - +
400D ALA 5.2 2.9 - - - +
401D GLY 4.9 1.1 - - - -
402D GLY* 3.4 33.9 - - - +
602D TPP 4.1 14.8 - - + +
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Residues in contact with GLY 74 (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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47B GLU* 2.9 48.4 - - - +
69B LEU* 4.1 4.7 - - - +
70B HIS 2.8 27.8 + - - -
73B ALA* 1.3 71.3 - - - +
75B THR* 1.3 65.5 + - - +
77B ASN 3.2 6.9 + - - -
78B ALA* 3.4 2.3 + - - +
602D TPP 4.3 3.0 - - - +
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Residues in contact with THR 75 (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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69B LEU* 4.2 14.1 - - + +
71B SER 3.1 16.6 + - - -
72B ALA 3.8 2.9 - - - -
74B GLY* 1.3 73.9 - - - +
76B GLY* 1.3 64.1 + - - +
78B ALA* 3.0 14.2 + - - +
79B MET* 3.4 22.8 + - - +
82B LEU* 5.0 4.4 - - + +
94B VAL* 5.7 0.4 - - + -
96B ALA* 3.4 7.3 - - - +
118B LEU* 3.8 20.9 - - + -
119B PRO* 4.7 3.1 - - + -
155B TYR* 2.7 47.9 + - + +
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Residues in contact with GLY 76 (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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72B ALA 2.6 21.8 + - - -
75B THR* 1.3 70.1 - - - +
77B ASN* 1.3 61.8 + - - +
78B ALA 2.9 6.3 + - - -
79B MET* 3.1 8.4 + - - -
118B LEU* 4.5 5.8 - - - +
76D GLY 3.0 21.8 - - - +
79D MET* 3.4 21.3 - - - +
80D GLY 3.3 11.6 + - - -
122D LEU* 5.8 0.2 - - - -
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Residues in contact with ASN 77 (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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46B GLN* 3.3 24.1 + - - +
47B GLU* 2.8 31.6 + - + +
48B ALA* 3.7 18.9 + - - +
73B ALA 3.0 11.7 + - - -
74B GLY 3.2 3.3 + - - +
76B GLY* 1.3 73.5 - - - +
78B ALA* 1.3 57.6 + - - +
79B MET 3.5 0.6 + - - -
46D GLN* 5.6 0.9 + - - -
48D ALA* 4.8 7.5 - - - +
76D GLY 4.7 0.9 - - - -
77D ASN* 4.5 19.9 - - - +
80D GLY* 3.3 22.3 + - - +
81D ALA 4.3 1.0 + - - -
403D LEU 4.1 6.7 + - - +
433D TYR* 4.0 6.3 - - - +
602D TPP 3.1 23.4 - - - +
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Residues in contact with ALA 78 (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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47B GLU* 3.8 10.5 - - + +
48B ALA* 4.2 7.0 - - - +
51B VAL* 3.6 26.9 - - + -
69B LEU* 4.1 8.7 - - + -
74B GLY 3.4 9.1 + - - +
75B THR* 3.0 10.0 + - - +
76B GLY 2.9 1.4 - - - -
77B ASN* 1.3 80.2 - - - +
79B MET* 1.3 58.2 + - - +
80B GLY 3.3 2.7 - - - -
81B ALA* 3.2 6.8 + - - +
82B LEU* 3.0 32.9 + - + +
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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