Contacts of the helix formed by residues 74 - 87 (chain A) in PDB entry 1ZY3
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 ALA 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A SER* 1.3 83.3 - - - +
75A GLN* 1.3 64.3 + - - +
76A GLN* 3.0 19.2 + - - +
77A ARG 2.8 17.5 + - - -
78A PHE* 3.3 16.2 + - - -
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Residues in contact with GLN 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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74A ALA* 1.3 77.8 - - + +
76A GLN* 1.3 66.9 + - - +
77A ARG 2.9 5.5 + - - -
78A PHE* 3.1 43.7 + - - +
79A THR* 2.8 29.9 + - - -
101A PHE* 4.9 0.5 - - - +
102A GLY* 5.5 0.2 - - - -
105A LEU* 3.2 38.7 - - + +
109A SER* 5.5 0.2 - - - +
117A LEU* 4.1 28.3 - - + -
121A VAL* 3.3 30.9 - - + +
124A TRP* 5.9 1.8 - - - -
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Residues in contact with GLN 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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73A SER* 5.6 2.0 - - - -
74A ALA* 3.0 23.9 - - + +
75A GLN* 1.3 79.0 + - - +
77A ARG* 1.3 56.2 + - - +
80A GLN* 3.1 28.6 - - - +
117A LEU* 4.0 25.1 - - - +
120A GLN* 4.8 5.1 + - - -
124A TRP* 3.8 38.0 - - + -
201B ILE* 5.5 0.7 - - - +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO 3.8 18.0 + - - -
72A GLY* 3.9 7.2 + - - -
73A SER* 3.0 46.1 + - - +
74A ALA 2.8 10.7 + - - +
76A GLN* 1.3 80.6 - - - +
78A PHE* 1.3 67.2 + - + +
80A GLN* 3.7 3.6 - - - -
81A VAL* 3.0 25.2 + - + +
201B ILE* 3.5 45.9 - - - +
202B ILE* 3.7 26.3 - - + +
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Residues in contact with PHE 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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64A ALA* 6.3 2.7 - - + -
72A GLY* 6.4 0.4 - - - -
73A SER 3.7 20.6 - - - -
74A ALA* 3.3 11.4 + - - -
75A GLN* 3.1 32.0 + - - +
77A ARG* 1.3 80.0 - - + +
79A THR* 1.3 62.0 + - - +
81A VAL* 3.1 27.1 - - - +
82A SER* 3.4 4.2 + - - -
101A PHE* 3.7 29.5 - + + -
105A LEU* 4.0 22.4 - - + -
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Residues in contact with THR 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 GLN* 2.8 35.6 + - - -
78A PHE* 1.3 75.5 - - - +
80A GLN* 1.3 63.5 + - - +
82A SER* 3.4 15.6 + - - +
83A ASP* 3.4 10.9 + - - +
98A PHE* 3.7 44.6 - - + +
101A PHE* 4.7 3.3 - - + +
102A GLY* 4.7 12.1 + - - +
121A VAL* 4.5 4.0 - - + +
124A TRP* 6.6 0.4 - - - -
125A MET* 4.8 11.2 - - + -
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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 GLN* 3.1 29.4 + - - +
77A ARG* 3.7 8.2 - - - +
78A PHE 3.1 0.6 - - - -
79A THR* 1.3 80.0 + - - +
81A VAL* 1.3 58.2 + - - +
82A SER 3.2 0.7 - - - -
83A ASP* 2.7 47.5 + - - +
84A GLU* 2.9 16.8 + - - +
98A PHE* 5.8 1.0 - - - -
124A TRP* 4.8 14.9 - - - -
128A TYR* 5.2 6.5 - - - -
201B ILE* 4.1 26.1 - - + +
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Residues in contact with VAL 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 ARG* 3.0 15.9 + - + +
78A PHE* 3.1 19.6 + - - +
80A GLN* 1.3 76.5 - - - +
82A SER* 1.3 65.5 + - - +
84A GLU* 3.4 6.6 - - + +
85A LEU* 3.8 1.0 + - - +
101A PHE* 4.1 15.3 - - + -
202B ILE* 4.3 17.5 - - + +
205B ILE* 3.9 20.0 - - + -
206B ALA* 3.2 34.4 - - + +
209B LEU* 3.7 32.7 - - + +
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Residues in contact with SER 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 PHE 3.4 10.6 + - - -
79A THR* 3.4 13.1 + - - -
80A GLN 3.2 0.4 - - - -
81A VAL* 1.3 78.0 - - - +
83A ASP* 1.3 63.1 + - - +
84A GLU 3.2 0.4 + - - -
85A LEU* 3.5 2.6 + - - +
86A PHE* 3.2 22.0 + - - +
94A ARG* 3.9 9.7 - - - +
97A ALA* 4.4 6.7 - - - -
98A PHE* 3.6 33.2 - - - -
101A PHE* 3.6 22.3 - - - +
209B LEU* 4.8 7.2 - - - -
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Residues in contact with ASP 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 THR 3.4 3.3 + - - +
80A GLN* 2.7 49.3 + - - +
82A SER* 1.3 76.8 - - - +
84A GLU* 1.3 66.1 + - - +
86A PHE* 3.0 18.5 + - - +
87A GLN* 2.7 35.4 + - - +
98A PHE* 3.6 21.5 - - + -
128A TYR* 2.6 34.3 + - + +
132A ARG* 5.1 0.2 - - - -
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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 2.9 18.2 + - - +
81A VAL* 3.4 13.5 - - + +
83A ASP* 1.3 78.9 - - - +
85A LEU* 1.3 59.7 + - - +
87A GLN* 3.5 20.7 + - - +
201B ILE* 2.6 40.5 + - - +
202B ILE* 2.8 15.1 + - + +
203B LYS* 2.7 73.0 + - + +
206B ALA* 3.6 13.9 - - + -
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Residues in contact with LEU 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 VAL 3.8 1.9 + - - +
82A SER* 3.5 5.4 + - - +
83A ASP 3.2 0.4 - - - -
84A GLU* 1.3 78.8 - - - +
86A PHE* 1.3 64.5 + - - +
87A GLN 3.1 2.5 - - - -
88A GLY* 3.0 24.8 + - - +
89A GLY* 3.0 16.5 + - - +
94A ARG* 3.7 26.2 - - - +
203B LYS* 3.8 17.9 - - + +
206B ALA* 3.7 15.5 - - + +
207B ARG* 3.5 31.9 - - + +
209B LEU* 5.8 1.1 - - + -
210B ALA* 3.7 22.2 - - + -
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Residues in contact with PHE 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 SER 3.2 18.0 + - - +
83A ASP* 3.0 15.4 + - - +
85A LEU* 1.3 77.4 - - - +
87A GLN* 1.3 59.7 + - - +
88A GLY 3.2 0.7 + - - -
89A GLY 3.6 7.9 + - - -
90A PRO* 3.6 44.5 - - + +
94A ARG* 3.4 29.4 - - + +
95A LEU* 3.7 33.2 - - + -
98A PHE* 3.8 23.3 - + + -
128A TYR* 4.6 6.7 - + + +
133A LEU* 3.7 40.2 - - + +
136A TRP* 5.5 4.3 + + + -
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Residues in contact with GLN 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 ASP* 2.7 41.5 + - - +
84A GLU* 3.5 20.2 + - - +
85A LEU 3.1 0.2 - - - -
86A PHE* 1.3 77.9 - - - +
88A GLY* 1.3 56.6 + - - +
90A PRO* 5.7 0.2 - - - -
128A TYR* 4.1 7.4 - - - +
132A ARG* 4.2 24.2 + - - +
203B LYS* 2.9 26.7 + - - -
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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