Contacts of the helix formed by residues 59 - 71 (chain A) in PDB entry 4ZDV
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 ASN 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A HIS 3.4 10.0 + - - +
58A VAL* 1.3 78.7 - - - +
60A MET* 1.3 66.5 + - - +
61A SER* 4.1 15.2 + - - +
62A GLU* 3.1 21.4 + - + +
63A LEU* 3.1 9.8 + - - +
92A SER* 3.1 31.2 + - - +
93A THR 3.6 4.7 - - - -
94A PRO* 4.1 9.2 - - - +
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Residues in contact with MET 60 (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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59A ASN* 1.3 71.8 - - - +
61A SER* 1.3 63.3 + - - +
63A LEU* 3.1 13.2 + - + +
64A VAL* 3.0 25.2 + - + +
81A LEU* 6.2 0.7 - - + -
83A VAL* 4.2 3.8 - - + -
88A MET* 3.8 37.0 - - + +
91A VAL* 3.4 23.8 + - + +
93A THR 3.0 20.5 + - - +
95A ILE* 3.7 28.3 - - + -
98A ILE* 3.6 30.5 - - + -
111A MET* 3.5 32.8 - - + -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 4.1 9.9 + - - +
60A MET* 1.3 73.1 - - - +
62A GLU* 1.3 60.3 + - - +
64A VAL* 3.4 5.3 + - - +
65A LYS* 3.0 36.5 + - - +
88A MET 3.6 2.9 - - - -
89A VAL 3.3 26.9 - - - +
90A SER* 4.1 4.5 - - - -
91A VAL 2.8 25.7 + - - -
92A SER* 4.4 3.8 - - - -
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Residues in contact with GLU 62 (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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58A VAL* 3.5 22.5 - - + +
59A ASN* 3.1 19.6 + - + +
61A SER* 1.3 80.8 + - - +
63A LEU* 1.3 66.0 + - - +
65A LYS* 3.2 17.6 + - - +
66A ILE* 3.1 36.3 + - + +
69A ARG* 5.1 6.1 + - - -
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Residues in contact with LEU 63 (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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33A VAL* 4.9 2.0 - - + -
35A ILE* 4.7 3.6 - - + -
52A PHE* 6.4 0.4 - - + -
54A VAL* 4.2 22.7 - - + -
58A VAL* 4.3 7.9 - - + -
59A ASN 3.1 9.7 + - - +
60A MET* 3.1 15.8 + - + +
62A GLU* 1.3 74.3 - - - +
64A VAL* 1.3 66.8 + - - +
66A ILE* 3.2 19.3 + - + +
67A ILE* 3.1 39.3 + - + +
81A LEU* 4.5 8.1 - - + -
95A ILE* 3.8 19.1 - - + -
111A MET* 3.6 36.3 - - + -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET 3.0 15.4 + - - +
61A SER 3.6 8.5 - - - +
62A GLU 3.2 0.4 - - - -
63A LEU* 1.3 75.8 - - - +
65A LYS* 1.3 59.2 + - + +
67A ILE* 3.4 0.7 + - - +
68A ARG* 3.0 28.0 + - + +
79A PHE* 3.7 26.6 - - + -
81A LEU* 3.9 22.7 - - + -
88A MET* 3.6 35.2 - - + +
89A VAL* 3.9 26.0 - - + +
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Residues in contact with LYS 65 (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 SER* 3.0 25.8 + - - +
62A GLU* 3.2 16.7 + - - +
64A VAL* 1.3 75.6 - - + +
66A ILE* 1.3 66.7 - - - +
68A ARG* 3.3 11.0 + - - +
69A ARG* 2.9 45.9 + - - +
89A VAL* 5.6 3.6 - - + +
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Residues in contact with ILE 66 (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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54A VAL* 6.0 1.8 - - + -
58A VAL* 5.0 7.4 - - + -
62A GLU* 3.1 35.8 + - + +
63A LEU* 3.2 23.1 + - + +
65A LYS* 1.3 76.3 - - - +
67A ILE* 1.3 69.7 + - + +
69A ARG* 3.4 24.2 + - - +
70A ARG* 3.0 31.2 + - + +
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Residues in contact with ILE 67 (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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35A ILE* 3.6 45.5 - - + -
47A LEU* 4.4 11.0 - - + -
52A PHE* 4.9 17.5 - - + -
63A LEU* 3.1 27.0 + - + +
64A VAL 3.9 3.6 - - - +
66A ILE* 1.3 81.8 - - + +
68A ARG* 1.3 67.8 + - - +
70A ARG* 3.1 8.5 + - - +
71A LEU* 3.1 31.1 + - + +
79A PHE* 3.8 19.7 - - + -
81A LEU* 4.1 9.9 - - + -
113A TYR* 4.9 1.8 - - + -
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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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64A VAL* 3.0 19.0 + - - +
65A LYS* 3.3 11.9 + - - +
67A ILE* 1.3 80.3 - - - +
69A ARG* 1.3 61.7 + - + +
71A LEU* 3.4 4.1 + - - +
72A GLN 3.3 13.0 + - - -
73A LEU* 3.4 40.5 + - + +
74A ASN 2.7 30.9 + - - -
75A PRO* 3.4 16.1 + - - +
77A GLN 2.8 25.7 + - - -
79A PHE* 3.6 32.7 - - + +
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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
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62A GLU* 5.1 6.3 + - - -
65A LYS* 2.9 36.5 + - - +
66A ILE* 3.6 33.2 - - - +
68A ARG* 1.3 73.5 - - + +
70A ARG* 1.3 61.7 + - - +
72A GLN* 2.9 26.3 + - - +
73A LEU 5.2 0.2 - - - +
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Residues in contact with ARG 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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47A LEU* 3.9 14.4 - - + +
48A ASP* 2.9 41.8 + - - +
49A LYS* 3.8 15.2 - - - +
52A PHE* 3.8 28.3 - - - -
66A ILE* 3.0 22.4 + - + +
67A ILE* 3.1 13.4 + - - +
69A ARG* 1.3 76.5 - - - +
71A LEU* 1.3 59.9 + - - +
72A GLN* 3.1 10.3 + - - +
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Residues in contact with LEU 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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44A LEU* 5.4 0.7 - - + -
45A PRO* 3.7 41.1 - - + +
46A VAL 4.3 1.3 - - - +
47A LEU* 3.6 29.8 - - + +
67A ILE* 3.1 20.7 + - + +
68A ARG 3.8 4.5 - - - +
69A ARG 3.2 0.2 - - - -
70A ARG* 1.3 73.2 - - - +
72A GLN* 1.3 70.9 + - - +
73A LEU* 3.3 22.3 + - + +
79A PHE* 3.5 35.7 - - + -
113A TYR* 3.7 20.2 - - + +
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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