Contacts of the helix formed by residues 74 - 88 (chain A) in PDB entry 4CCZ
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 GLN 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PHE* 4.6 7.0 - - + +
70A LEU* 2.8 33.6 + - + +
73A THR* 1.3 82.6 - - - +
75A PRO* 1.3 66.0 - - - +
76A ASP* 3.4 2.7 - - - -
77A VAL* 3.2 34.3 + - + +
78A ILE* 3.4 5.2 + - - +
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Residues in contact with PRO 75 (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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70A LEU 3.3 5.6 - - - +
71A SER* 3.5 17.9 - - - +
72A ILE 3.3 19.1 - - - +
73A THR 3.6 2.7 - - - +
74A GLN* 1.3 88.5 - - - +
76A ASP* 1.3 59.7 + - + +
78A ILE* 3.1 5.6 + - + +
79A TYR* 2.9 30.1 + - - +
124A VAL* 3.9 15.7 - - + +
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Residues in contact with ASP 76 (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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74A GLN 3.4 1.0 - - - -
75A PRO* 1.3 80.7 - - + +
77A VAL* 1.3 64.6 + - + +
79A TYR* 3.6 10.1 - - + +
80A GLN* 3.0 25.3 + - - +
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Residues in contact with VAL 77 (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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41A ILE* 5.4 7.2 - - + -
44A GLU* 4.7 20.2 - - + -
70A LEU* 5.7 3.6 - - + -
74A GLN* 3.2 25.5 + - + +
75A PRO 3.2 0.6 - - - -
76A ASP* 1.3 80.4 - - + +
78A ILE* 1.3 72.0 + - + +
80A GLN* 3.3 5.5 + - - +
81A ILE* 3.1 20.5 + - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 5.9 2.0 - - + -
41A ILE* 3.8 33.9 - - + -
70A LEU* 3.9 28.0 - - + +
71A SER* 4.1 8.1 - - - +
74A GLN 3.4 11.2 + - - +
75A PRO* 3.1 7.9 + - + +
77A VAL* 1.3 77.1 - - + +
79A TYR* 1.3 65.6 + - - +
81A ILE* 3.1 11.1 + - + +
82A HIS* 3.0 42.7 + - + -
96A ASN* 3.9 25.6 - - + +
121A SER* 6.1 0.4 - - - +
124A VAL* 4.1 10.3 - - + -
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Residues in contact with TYR 79 (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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75A PRO 2.9 17.0 + - - +
76A ASP* 3.6 10.8 - - - +
78A ILE* 1.3 76.7 - - - +
80A GLN* 1.3 61.3 + - + +
82A HIS* 3.2 8.7 + - - +
83A LYS* 3.0 32.9 + - + +
124A VAL* 3.7 29.3 - - + +
127A LYS* 3.8 13.8 + - + -
128A ALA* 3.6 27.7 - - + +
131A GLU* 3.9 20.8 - - + +
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP 3.0 17.9 + - - +
77A VAL* 3.7 6.3 - - - +
79A TYR* 1.3 78.4 - - + +
81A ILE* 1.3 65.5 + - - +
83A LYS* 3.6 8.3 - - - +
84A GLU* 3.2 34.3 + - + +
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Residues in contact with ILE 81 (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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37A MET* 5.6 8.3 - - + -
40A MET* 4.8 18.2 - - + -
41A ILE* 6.1 3.1 - - + -
77A VAL* 3.1 13.6 + - + +
78A ILE* 3.1 18.5 + - + +
80A GLN* 1.3 77.9 - - - +
82A HIS* 1.3 63.4 + - + +
84A GLU* 3.5 10.6 + - - +
85A TYR* 3.1 32.1 + - + -
328A PRO* 6.2 0.4 - - - -
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Residues in contact with HIS 82 (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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34A ASP* 4.3 10.3 - - - -
37A MET* 6.5 1.1 - - + -
78A ILE* 3.0 36.6 + - + +
79A TYR* 3.5 7.6 - - - +
81A ILE* 1.3 75.8 - - + +
83A LYS* 1.3 66.2 + - - +
85A TYR* 3.1 9.3 + + + +
86A LEU* 2.9 29.5 + - + +
93A ILE* 4.2 16.4 - - + -
94A GLU 3.1 24.7 + - - -
96A ASN* 4.9 7.4 + - + +
121A SER 4.9 3.1 - - - -
124A VAL* 4.1 3.6 + - + -
125A ALA* 3.5 37.5 + - + +
128A ALA* 3.7 14.4 - - + -
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Residues in contact with LYS 83 (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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79A TYR* 3.0 23.6 + - + +
80A GLN* 3.6 12.6 - - - +
82A HIS* 1.3 74.4 - - - +
84A GLU* 1.3 64.7 + - - +
86A LEU* 3.1 12.3 + - - +
87A LEU* 2.9 26.7 + - - +
128A ALA* 4.5 3.1 - - + +
132A VAL* 6.3 0.4 - - - -
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Residues in contact with GLU 84 (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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80A GLN* 3.2 17.8 + - + +
81A ILE* 3.7 11.7 - - - +
82A HIS 3.3 0.2 - - - -
83A LYS* 1.3 78.1 - - + +
85A TYR* 1.3 58.4 + - - +
87A LEU* 3.7 4.2 + - - +
88A ALA* 2.9 29.8 + - - +
328A PRO* 3.7 29.2 - - + +
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Residues in contact with TYR 85 (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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34A ASP* 3.8 27.6 - - + +
35A GLY* 3.5 33.5 - - - -
36A GLY 3.3 14.1 + - - -
37A MET* 5.1 7.9 - - + -
40A MET* 4.7 9.0 + - + +
81A ILE* 3.1 31.1 + - + -
82A HIS* 3.1 9.6 + + + +
84A GLU* 1.3 75.3 - - - +
86A LEU* 1.3 67.9 + - + +
88A ALA* 3.0 23.1 + - - -
91A ASP* 4.7 5.5 - - - +
326A SER 3.2 19.9 + - - -
327A THR* 3.4 6.6 - - - -
328A PRO* 3.3 43.4 - - + +
331A ILE* 4.3 11.3 - - + +
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Residues in contact with LEU 86 (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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82A HIS* 2.9 22.9 + - + +
83A LYS* 3.6 7.4 - - - +
85A TYR* 1.3 78.4 - - + +
87A LEU* 1.3 61.1 + - - +
88A ALA 4.4 1.9 - - - -
91A ASP* 4.2 14.2 - - + +
92A ILE 5.2 0.7 - - - -
93A ILE* 4.2 25.1 - - + +
128A ALA* 3.3 47.6 - - + +
129A ALA* 3.6 3.8 - - + +
132A VAL* 3.7 16.4 - - + -
140A ARG* 2.8 56.7 + - + -
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Residues in contact with LEU 87 (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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83A LYS 2.9 15.6 + - - +
84A GLU* 4.1 4.3 - - - +
86A LEU* 1.3 76.8 - - - +
88A ALA* 1.3 62.8 + - - +
132A VAL* 5.1 2.8 - - + +
140A ARG* 4.9 3.5 + - - +
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Residues in contact with ALA 88 (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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84A GLU 2.9 20.9 + - - +
85A TYR* 3.0 17.0 + - - +
86A LEU 4.4 2.7 - - - -
87A LEU* 1.3 81.5 - - - +
91A ASP* 6.1 1.6 - - - -
328A PRO* 3.3 29.4 - - + +
331A ILE* 4.7 7.0 - - + -
332A ARG* 3.8 21.9 - - + +
335A ALA* 3.8 23.2 - - - +
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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