Contacts of the helix formed by residues 69 - 81 (chain A) in PDB entry 4GL5
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 GLY 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A PHE 2.8 17.6 + - - -
66A LEU 4.5 1.5 - - - -
67A TRP 3.6 0.8 - - - -
68A MET* 1.3 73.8 - - - +
70A ILE* 1.3 68.5 + - - -
71A GLY 2.8 5.5 + - - -
72A SER* 2.9 14.2 + - - -
73A ALA* 3.0 10.9 + - - +
475A HIS 3.4 8.1 - - - -
476A ASP* 3.3 16.4 - - - -
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Residues in contact with ILE 70 (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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65A PHE* 3.7 28.6 + - + +
69A GLY* 1.3 69.8 - - - +
71A GLY* 1.3 60.5 + - - +
73A ALA 3.8 0.3 + - - -
74A CYS* 2.9 32.6 + - - -
89A ILE* 5.7 0.7 - - + -
225A GLN 4.6 10.8 - - - +
228A LEU* 5.0 5.6 - - + -
229A ILE* 3.7 36.6 - - + -
372A LEU* 4.5 12.6 - - + -
374A MET* 4.8 11.2 - - + -
395A ILE* 4.2 16.6 - - + -
476A ASP* 3.0 23.6 + - - +
477A LEU* 4.3 26.0 - - + +
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Residues in contact with GLY 71 (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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69A GLY 2.8 2.4 + - - -
70A ILE* 1.3 78.6 - - - +
72A SER* 1.3 60.7 + - - -
74A CYS* 3.5 5.5 + - - +
75A ASN* 3.3 15.9 + - - -
372A LEU* 3.4 19.4 - - - +
397A ASN* 5.2 0.2 + - - -
475A HIS* 3.1 31.1 + - - -
476A ASP 2.9 15.0 + - - -
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Residues in contact with SER 72 (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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68A MET* 3.2 37.8 + - - +
69A GLY 2.9 6.8 + - - -
71A GLY* 1.3 70.7 - - - -
73A ALA* 1.3 56.8 + - - +
75A ASN* 3.1 5.8 + - - +
76A TYR* 2.7 36.7 + - - +
475A HIS* 3.3 27.5 + - - +
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Residues in contact with ALA 73 (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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64A ARG* 4.6 1.8 - - + -
65A PHE* 3.7 49.6 - - + +
68A MET* 4.0 18.6 - - + -
69A GLY 3.0 12.4 + - - +
72A SER* 1.3 77.6 + - - +
74A CYS* 1.3 57.7 + - - +
76A TYR* 3.3 1.4 + - - +
77A TYR* 2.9 39.9 + - + -
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Residues in contact with CYS 74 (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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65A PHE* 3.9 17.9 - - - -
70A ILE 2.9 24.2 - - - -
71A GLY 3.6 5.2 - - - +
72A SER 3.2 0.4 - - - -
73A ALA* 1.3 73.3 - - - +
75A ASN* 1.3 64.9 + - - +
77A TYR* 3.3 0.4 + - - -
78A ASN* 2.9 32.9 + - - +
96A ILE* 3.6 15.2 - - + +
372A LEU* 3.9 9.4 - - + -
395A ILE* 3.8 31.2 - - + -
397A ASN* 3.7 16.2 - - + +
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Residues in contact with ASN 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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71A GLY 3.3 5.7 + - - +
72A SER* 3.1 10.9 + - - +
74A CYS* 1.3 78.6 - - - +
76A TYR* 1.3 61.4 + - - +
78A ASN* 4.3 1.0 - - - +
79A ARG* 3.3 31.1 + - - +
371A ASP* 3.9 7.9 + - - -
397A ASN* 3.9 11.1 + - - +
399A GLY 5.9 1.4 - - - -
400A ARG* 3.3 37.5 + - - +
475A HIS* 3.1 30.7 - - + +
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Residues in contact with TYR 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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64A ARG* 3.1 49.4 + - - -
68A MET* 4.1 20.6 - - + -
72A SER 2.7 19.9 + - - +
73A ALA 3.4 4.3 - - - +
74A CYS 3.1 0.2 - - - -
75A ASN* 1.3 73.6 - - - +
77A TYR* 1.3 94.3 + + - +
79A ARG* 3.1 32.9 + - - +
80A VAL* 3.1 54.3 + - + +
81A TYR* 5.2 1.2 - + - -
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Residues in contact with TYR 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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50A PRO* 4.6 10.3 - - + -
60A ILE* 4.0 10.0 - - + +
61A SER* 3.3 22.9 - - - -
64A ARG* 3.2 40.3 + - + +
65A PHE* 4.0 21.1 - + - -
73A ALA* 2.9 30.1 + - + +
76A TYR* 1.3 87.2 - + - +
78A ASN* 1.3 60.2 + - - +
80A VAL 4.1 0.2 - - - -
81A TYR* 3.1 46.3 + + - +
85A MET* 3.5 32.9 - - + +
87A VAL* 4.0 17.0 - - + -
96A ILE* 3.9 9.0 - - + -
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Residues in contact with ASN 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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74A CYS* 2.9 14.0 + - - +
75A ASN 4.3 0.4 - - - +
77A TYR* 1.3 74.0 - - - +
79A ARG* 1.3 60.9 + - - +
81A TYR 2.8 21.0 - - - +
82A GLY 3.0 9.3 + - - +
83A GLU* 2.8 40.2 + - - +
96A ILE* 3.2 33.5 + - - +
98A SER* 3.7 13.9 + - - +
397A ASN* 2.9 31.1 + - - +
400A ARG* 3.4 15.9 + - - +
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Residues in contact with ARG 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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68A MET* 6.0 0.4 - - - +
75A ASN* 3.3 32.1 + - - +
76A TYR* 3.1 39.8 + - - +
78A ASN* 1.3 80.7 - - - +
80A VAL* 1.3 67.5 + - + +
81A TYR 3.5 4.0 - - - +
400A ARG* 3.6 24.5 + - - +
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Residues in contact with VAL 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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76A TYR* 3.1 51.8 + - + +
79A ARG* 1.3 82.1 - - + +
81A TYR* 1.3 87.4 + - + +
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Residues in contact with TYR 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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48A PRO* 4.9 1.6 - - + -
49A GLY* 3.3 37.7 - - - +
50A PRO* 3.3 25.1 - - + +
76A TYR* 5.2 1.6 - + - -
77A TYR* 3.1 41.0 + + - +
78A ASN 2.8 11.8 - - - +
79A ARG 3.5 4.0 - - - +
80A VAL* 1.3 102.2 - - + +
82A GLY* 1.3 65.1 + - - +
83A GLU* 5.3 0.3 - - - -
85A MET* 3.6 22.0 - - + -
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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