Contacts of the helix formed by residues 67 - 82 (chain A) in PDB entry 4Z4H
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 PRO 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS 3.7 0.4 - - - +
66A CYS* 1.3 89.1 - - + +
68A ARG* 1.3 66.3 + - - +
69A ARG* 3.1 8.1 - - + +
70A VAL* 3.1 23.8 + - + +
71A ASN* 3.2 10.6 + - - +
16B U 3.8 24.0 - - - +
17B C 3.2 64.8 - - + +
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Residues in contact with ARG 68 (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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66A CYS 3.7 0.8 + - - -
67A PRO* 1.3 73.1 - - - +
69A ARG* 1.3 62.1 + - - +
71A ASN* 3.3 13.2 + - - +
72A ARG* 3.3 33.1 + - - +
95A ASP* 2.7 43.6 + - - -
96A GLY* 3.5 23.0 - - - +
97A ARG* 2.8 31.2 - - + +
14B A 2.4 35.8 + - - -
15B G 3.1 42.1 + - - +
16B U 4.0 8.7 + - - +
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 3.1 6.1 - - + +
68A ARG* 1.3 79.9 - - - +
70A VAL* 1.3 63.4 + - + +
72A ARG* 3.2 15.2 + - - +
73A GLU* 3.1 54.8 + - - +
76A GLU* 4.4 6.5 + - - -
171A SER 3.7 20.5 + - - -
172A MET* 3.2 48.5 + - - +
174A TYR 5.4 1.4 + - - -
176A PRO* 5.7 4.9 - - - -
15B G 5.4 0.6 + - - -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A CYS* 3.9 22.7 - - + -
67A PRO* 3.1 24.5 + - + +
69A ARG* 1.3 80.3 - - + +
71A ASN* 1.3 55.8 + - - +
73A GLU* 3.2 11.2 + - + +
74A ILE* 3.0 38.7 + - + +
119A LEU* 5.1 7.4 - - + -
128A PHE* 4.5 7.6 - - + -
17B C 3.7 32.8 - - + +
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Residues in contact with ASN 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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61A ILE* 3.8 27.0 - - + +
63A PRO 5.4 0.3 - - - +
64A GLU* 5.6 8.2 + - - +
66A CYS* 3.3 31.5 + - - +
67A PRO 3.2 8.0 + - - +
68A ARG* 3.5 3.5 - - - +
69A ARG 3.2 0.4 - - - -
70A VAL* 1.3 75.1 - - - +
72A ARG* 1.3 64.8 + - - +
74A ILE* 3.4 10.5 + - - +
75A VAL* 3.1 28.1 + - - +
94A PHE* 3.8 4.0 - - + -
96A GLY 3.3 27.5 + - - +
97A ARG* 4.1 10.7 + - - +
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 3.4 35.1 + - - +
69A ARG* 3.2 22.2 + - - +
71A ASN* 1.3 73.8 - - - +
73A GLU* 1.3 56.5 + - - +
75A VAL* 3.4 1.6 + - - +
76A GLU* 2.7 36.4 + - - +
94A PHE* 2.8 38.4 + - + +
95A ASP* 3.3 21.6 + - - +
96A GLY* 3.7 10.3 - - - +
167A ARG* 5.5 3.2 - - - +
168A HIS* 4.8 11.5 + - + +
171A SER* 3.6 45.5 + - - -
172A MET* 4.2 17.9 - - + +
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Residues in contact with GLU 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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69A ARG* 3.1 40.4 + - + +
70A VAL* 3.3 14.6 - - + +
72A ARG* 1.3 73.8 - - - +
74A ILE* 1.3 66.1 + - - +
76A GLU* 3.1 23.1 + - - +
77A HIS* 3.0 33.1 + - - +
119A LEU* 4.1 25.3 - - + +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.6 19.5 - - + -
70A VAL* 3.0 19.7 + - + +
71A ASN* 3.5 14.8 - - - +
72A ARG 3.3 0.2 - - - -
73A GLU* 1.3 76.7 - - - +
75A VAL* 1.3 58.4 + - + +
77A HIS* 3.6 3.1 + - - +
78A MET* 2.9 30.1 + - - +
117A VAL* 3.7 16.0 - - + +
119A LEU* 4.3 11.9 - - + -
128A PHE* 3.6 49.4 - - + -
130A VAL* 3.6 30.5 - - + -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.8 19.5 - - + -
61A ILE* 4.5 8.3 - - + -
71A ASN 3.1 16.5 + - - +
72A ARG 4.0 1.3 - - - +
74A ILE* 1.3 74.6 - - + +
76A GLU* 1.3 67.6 + - - +
78A MET* 3.8 20.6 - - + -
79A VAL* 2.9 35.3 + - + +
92A PRO* 5.9 0.7 - - + -
94A PHE* 3.6 35.9 - - + -
100A LEU* 4.2 15.0 - - + -
130A VAL* 5.5 0.2 - - + -
168A HIS* 6.0 2.7 - - + -
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Residues in contact with GLU 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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69A ARG* 4.4 5.9 + - - -
72A ARG 2.7 21.1 + - - +
73A GLU* 3.1 29.4 + - - +
75A VAL* 1.3 76.0 - - - +
77A HIS* 1.3 75.5 + - + +
79A VAL* 3.4 10.0 + - - +
80A GLN* 3.5 17.4 + - - +
172A MET* 4.3 23.3 - - + +
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Residues in contact with HIS 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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73A GLU* 3.0 20.0 + - - +
74A ILE* 4.2 2.9 - - - +
76A GLU* 1.3 85.0 - - + +
78A MET* 1.3 58.6 + - - +
79A VAL 3.0 2.7 - - - -
80A GLN* 2.9 26.4 + - - +
81A HIS* 2.6 62.3 + + + +
117A VAL* 6.1 1.1 - - + -
118A THR 4.1 7.9 + - - +
119A LEU* 3.3 36.7 - - + +
120A PRO* 4.5 9.1 - - + +
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Residues in contact with MET 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.6 4.5 - - + -
74A ILE* 2.9 22.2 + - + +
75A VAL* 3.7 35.9 - - + +
77A HIS* 1.3 76.7 - - - +
79A VAL* 1.3 61.3 + - + +
81A HIS* 4.0 2.4 - - - -
82A PHE* 3.1 33.8 + - + +
87A PHE* 3.5 24.7 - - + -
100A LEU* 5.0 1.3 - - + -
115A LEU* 3.8 23.6 - - + -
117A VAL* 3.4 32.0 - - + +
130A VAL* 4.0 21.8 - - + -
132A ILE* 4.2 8.5 - - + -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 2.9 39.0 + - + +
76A GLU* 3.7 5.4 - - - +
77A HIS 3.0 0.2 - - - -
78A MET* 1.3 80.4 - - + +
80A GLN* 1.3 63.2 + - + +
82A PHE 3.7 1.7 - - - -
83A LYS* 3.3 20.8 + - - +
87A PHE* 3.6 38.9 - - + +
90A ARG 4.7 4.0 - - - +
92A PRO* 4.0 30.7 - - + -
100A LEU* 5.2 0.4 - - + -
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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
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76A GLU* 3.5 11.3 + - - +
77A HIS* 2.9 38.5 + - - +
79A VAL* 1.3 77.2 - - + +
81A HIS* 1.3 82.1 + - - +
82A PHE 3.1 2.5 + - - -
83A LYS* 3.3 19.2 + - - +
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Residues in contact with HIS 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 HIS* 2.6 50.5 + + + +
78A MET* 4.5 1.6 - - - -
80A GLN* 1.3 93.5 + - - +
82A PHE* 1.3 79.7 + + + +
83A LYS 3.6 0.2 - - - -
117A VAL* 5.4 2.2 - - + -
118A THR* 3.7 31.3 + - - -
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Residues in contact with PHE 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 MET* 3.1 29.2 + - + +
79A VAL 3.7 4.3 - - - -
80A GLN 3.1 0.4 - - - -
81A HIS* 1.3 95.1 - + + +
83A LYS* 1.3 64.3 + - - +
84A THR 3.2 10.6 + - - +
86A ILE* 3.4 36.2 - - + +
87A PHE* 3.4 5.8 + - + +
115A LEU* 3.7 32.8 - - + -
116A GLU 3.5 28.7 - - - -
117A VAL* 4.1 15.7 - - + -
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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