Contacts of the helix formed by residues 63 - 75 (chain A) in PDB entry 3VTU
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A HIS 3.5 3.2 + - - +
62A VAL* 1.3 79.0 - - - +
64A MET* 1.4 69.2 + - - +
65A SER* 2.7 28.9 + - - -
66A GLU* 2.9 35.4 + - - +
67A LEU* 3.0 18.7 + - - +
96A SER* 3.4 29.4 + - - +
97A THR 3.6 10.1 - - - +
98A PRO* 4.4 2.0 - - + -
99A ILE 4.4 0.2 - - - +
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Residues in contact with MET 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 1.4 76.7 - - - +
65A SER* 1.4 61.0 + - - +
67A LEU* 3.7 11.6 - - + +
68A ILE* 2.9 35.9 + - - +
85A LEU* 5.2 1.8 - - - -
92A MET* 3.3 47.3 - - + +
93A VAL 5.2 0.2 - - - +
95A VAL* 3.6 33.7 - - + -
96A SER* 4.5 3.4 - - - +
97A THR 4.1 1.8 + - - +
99A ILE* 3.5 49.1 - - + +
102A VAL* 4.1 6.1 - - + -
115A MET* 4.2 13.9 - - - +
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Residues in contact with SER 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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63A ASN* 2.7 25.4 + - - -
64A MET* 1.4 78.7 - - - +
66A GLU* 1.3 65.2 + - - +
68A ILE* 3.5 11.0 + - - +
69A LYS* 3.2 21.0 + - - +
93A VAL* 5.1 12.0 + - - -
96A SER* 5.1 8.7 - - - +
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Residues in contact with GLU 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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61A HIS* 4.3 5.4 + - - +
62A VAL* 3.4 19.0 - - + +
63A ASN* 2.9 48.7 + - - +
65A SER* 1.3 81.1 - - - +
67A LEU* 1.3 61.1 + - - +
69A LYS* 3.2 10.1 + - - +
70A ILE* 3.1 32.0 + - + +
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Residues in contact with LEU 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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37A VAL* 5.3 0.2 - - + -
39A ILE* 4.4 8.7 - - + -
56A PHE* 5.9 1.6 - - + -
58A VAL* 4.5 22.7 - - + -
62A VAL* 4.1 4.7 - - + +
63A ASN 3.0 16.3 + - - +
64A MET* 3.7 11.7 - - + +
66A GLU* 1.3 71.2 - - - +
68A ILE* 1.3 66.9 + - - +
70A ILE* 3.1 19.4 + - + +
71A ILE* 3.0 41.2 + - + +
85A LEU* 4.2 10.8 - - + -
99A ILE* 4.2 14.6 - - + -
115A MET* 3.7 38.4 - - + -
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 2.9 22.9 + - + +
65A SER* 3.7 8.1 - - - +
66A GLU 3.4 0.2 - - - -
67A LEU* 1.3 74.9 - - - +
69A LYS* 1.4 63.7 + - - +
71A ILE* 3.3 2.1 + - - +
72A ARG* 2.9 43.5 + - - +
83A PHE* 4.0 21.7 - - + +
85A LEU* 4.0 30.5 - - + +
92A MET 4.4 2.2 - - - -
93A VAL* 3.8 41.5 - - + +
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Residues in contact with LYS 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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65A SER 3.2 13.3 + - - +
66A GLU* 3.2 12.5 + - - +
68A ILE* 1.4 78.2 - - - +
70A ILE* 1.3 59.4 - - + +
72A ARG* 3.4 8.4 + - - +
73A ARG* 3.0 56.3 + - + +
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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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56A PHE* 5.5 4.3 - - + -
58A VAL* 6.3 1.1 - - + -
62A VAL* 4.7 14.4 - - + -
66A GLU* 3.1 23.1 + - + +
67A LEU* 3.1 18.4 + - + +
69A LYS* 1.3 78.1 - - + +
71A ILE* 1.3 68.9 + - + +
73A ARG* 3.3 29.1 + - - +
74A ARG* 2.9 37.6 + - + +
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Residues in contact with ILE 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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39A ILE* 3.5 39.3 - - + -
51A LEU* 4.2 16.6 - - + -
56A PHE* 4.1 22.0 - - + -
67A LEU* 3.0 28.3 + - + +
68A ILE 4.1 0.2 - - - +
70A ILE* 1.3 78.4 - - + +
72A ARG* 1.3 66.4 + - - +
74A ARG* 3.2 4.3 + - - +
75A LEU* 2.9 31.9 + - + +
83A PHE* 3.4 34.3 - - + -
85A LEU* 5.1 4.5 - - + -
117A TYR* 4.7 1.3 - - + -
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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
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68A ILE* 2.9 35.5 + - - +
69A LYS* 3.8 7.6 - - - +
71A ILE* 1.3 76.9 - - - +
73A ARG* 1.4 60.6 + - - +
75A LEU* 3.5 0.8 + - - -
76A GLN 3.1 3.3 + - - -
77A LEU* 3.0 51.3 + - + +
78A ASN 3.0 25.1 + - - -
79A ALA* 4.0 8.5 + - - +
81A GLN 2.9 29.7 + - - -
82A ALA* 4.4 0.6 - - - +
83A PHE* 3.3 43.6 + - + +
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Residues in contact with ARG 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 LYS* 3.0 50.5 + - + +
70A ILE* 3.4 35.7 - - - +
72A ARG* 1.4 75.8 - - - +
74A ARG* 1.3 67.9 + - - +
76A GLN* 3.0 20.8 + - - +
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Residues in contact with ARG 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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51A LEU* 3.7 12.5 - - + +
52A ASP* 2.8 43.7 + - - +
53A LYS* 3.8 36.1 - - - +
56A PHE* 3.6 27.1 - - - -
70A ILE* 2.9 27.8 + - + +
71A ILE* 3.2 6.9 + - - +
73A ARG* 1.3 79.2 - - + +
75A LEU* 1.4 61.4 + - - +
76A GLN* 3.5 6.9 + - - +
205A SO4 3.5 12.6 + - - -
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Residues in contact with LEU 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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48A LEU* 5.2 0.9 - - + -
49A PRO* 3.6 24.8 - - + +
50A VAL 3.9 4.9 - - - +
51A LEU* 3.6 30.1 - - + -
71A ILE* 2.9 22.2 + - + +
73A ARG 3.2 0.2 - - - -
74A ARG* 1.4 74.0 - - - +
76A GLN* 1.4 69.7 + - - +
77A LEU* 3.4 24.9 + - + +
83A PHE* 3.6 36.6 - - + -
117A TYR* 3.6 29.2 - - + +
205A SO4 3.4 16.7 + - - +
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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