Contacts of the helix formed by residues 77 - 89 (chain A) in PDB entry 5CXV
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 PHE 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.0 19.8 + - + +
76A THR* 1.3 113.6 - - + +
78A SER* 1.3 69.8 + - - +
79A MET 3.6 1.1 - - - -
80A ASN* 3.4 3.6 + - - +
81A LEU* 3.0 46.4 + - + +
101A TRP* 5.5 1.3 - - + -
104A LEU* 3.8 31.4 - - + -
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Residues in contact with SER 78 (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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73A ILE* 3.7 5.6 + - - +
74A ILE* 3.1 22.9 + - - +
77A PHE* 1.3 78.1 - - - +
79A MET* 1.3 65.1 + - - +
82A TYR* 2.9 27.7 + - - +
101A TRP* 3.8 12.3 + - - +
104A LEU* 5.0 1.2 - - - +
105A ASP* 2.7 46.1 + - - +
408A TYR* 3.9 9.0 - - - -
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Residues in contact with MET 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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32A THR* 5.2 5.2 - - - +
35A LEU* 3.4 22.9 - - + -
36A SER* 3.5 29.2 - - - -
39A THR* 3.4 25.8 - - + +
74A ILE* 3.2 18.0 + - + +
75A GLY* 3.6 16.8 - - - +
78A SER* 1.3 74.2 - - - +
80A ASN* 1.3 58.7 + - - +
82A TYR* 4.2 0.2 - - - +
83A THR* 2.4 39.2 + - - +
405A TRP* 5.5 2.9 - - - +
408A TYR* 3.4 54.7 - - + +
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Residues in contact with ASN 80 (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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32A THR* 4.6 7.9 + - - -
33A GLY* 4.6 7.7 - - - -
36A SER* 2.6 36.4 + - - -
75A GLY 3.5 8.8 - - - +
76A THR* 3.5 12.1 - - - +
77A PHE 3.4 6.2 + - - +
78A SER 3.1 1.0 - - - -
79A MET* 1.3 76.5 - - - +
81A LEU* 1.3 61.0 + - + +
83A THR* 4.1 2.6 - - - -
84A THR* 2.7 39.5 + - - +
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Residues in contact with LEU 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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77A PHE* 3.0 40.8 + - + +
80A ASN* 1.3 76.5 - - + +
82A TYR* 1.3 57.5 + - - +
84A THR* 3.8 4.6 - - - -
85A TYR* 2.9 32.7 + - - +
91A TRP* 4.2 13.4 - - + -
93A LEU* 4.0 27.6 - - + -
101A TRP* 3.6 37.5 - - + +
104A LEU* 6.4 0.2 - - + -
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Residues in contact with TYR 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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78A SER 2.9 17.7 + - - +
79A MET 4.2 0.2 - - - +
81A LEU* 1.3 78.5 - - - +
83A THR* 1.3 56.5 - - - +
85A TYR* 3.9 11.7 - + - +
86A LEU* 2.9 52.2 + - + +
101A TRP* 3.5 29.9 - + + -
401A GLU* 3.2 31.5 + - - +
404A TYR* 3.4 35.7 - + - +
405A TRP* 4.0 25.8 - + + -
408A TYR* 3.7 23.8 - + + +
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Residues in contact with THR 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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28A ILE* 4.0 17.9 - - + +
29A GLY* 4.8 1.1 - - - -
32A THR* 3.2 28.5 + - + +
79A MET 2.4 25.4 + - - -
80A ASN* 4.1 3.8 - - - -
82A TYR* 1.3 78.6 - - - +
84A THR* 1.3 58.4 + - - +
86A LEU* 3.8 6.6 - - + +
87A LEU* 2.9 54.0 + - + +
405A TRP* 3.9 19.6 + - + +
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Residues in contact with THR 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 ASN* 2.7 23.8 + - - +
81A LEU* 3.8 5.6 - - - -
83A THR* 1.3 74.0 - - - +
85A TYR* 1.3 61.1 + - - +
87A LEU* 3.2 6.3 + - - -
88A MET* 2.9 50.0 + - + +
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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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81A LEU 2.9 18.3 + - - +
82A TYR* 4.0 18.6 - + - +
84A THR* 1.3 76.6 - - - +
86A LEU* 1.3 64.0 + - + +
88A MET* 4.9 0.2 - - - -
89A GLY* 2.9 29.0 + - - -
90A HIS* 3.3 35.0 + - - +
91A TRP* 3.3 47.6 - + + -
101A TRP* 4.9 6.7 - + - -
176A GLY 3.9 4.0 - - - -
177A GLN* 3.2 23.0 + - - +
178A CYS* 3.6 30.0 + - + -
179A TYR* 5.4 1.9 - - - -
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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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20A LYS* 3.7 38.1 + - - +
28A ILE* 5.0 10.1 - - + -
82A TYR* 2.9 54.7 + - + +
83A THR* 3.8 6.1 - - + +
85A TYR* 1.3 85.3 - - + +
87A LEU* 1.3 75.0 + - + +
89A GLY* 3.6 8.0 + - - -
401A GLU* 3.7 28.5 - - + +
405A TRP* 5.7 2.7 - - + -
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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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20A LYS* 3.4 31.3 - - + +
25A VAL* 3.7 54.8 - - + +
28A ILE* 3.8 28.3 - - + -
29A GLY* 3.8 12.1 - - - +
83A THR* 2.9 42.8 + - + +
84A THR* 3.9 5.6 - - - +
86A LEU* 1.3 82.1 - - + +
88A MET* 1.3 72.0 + - + +
89A GLY* 4.6 0.2 - - - -
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Residues in contact with MET 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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25A VAL* 4.4 18.8 - - + -
84A THR* 2.9 34.3 + - + +
85A TYR* 4.9 0.4 - - - -
87A LEU* 1.3 91.9 - - + +
89A GLY* 1.3 60.4 + - - +
90A HIS* 3.4 34.9 + - + +
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Residues in contact with GLY 89 (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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85A TYR* 2.9 17.0 + - - -
86A LEU* 4.1 6.7 - - - -
87A LEU 3.3 2.8 - - - -
88A MET* 1.3 77.3 - - - +
90A HIS* 1.3 61.7 + - - +
177A GLN* 3.8 15.8 + - - +
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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