Contacts of the strand formed by residues 59 - 70 (chain A) in PDB entry 3SVM
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 PHE 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLU 3.6 18.6 - - - -
57A ASP* 3.5 31.2 - - + -
58A VAL* 1.3 79.1 - - - +
60A GLU* 1.3 65.0 + - - +
61A VAL 3.5 0.5 + - - -
80A TRP* 3.7 21.8 - - + -
83A TYR* 3.7 31.0 - + + -
44P THR* 3.3 6.5 - - - -
45P ALA 3.1 30.0 + - - +
47P MLY 3.9 42.2 - - + -
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Residues in contact with GLU 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 PHE* 1.3 74.5 - - - +
61A VAL* 1.3 73.7 + - - +
62A GLU* 4.8 0.2 - - - -
80A TRP* 3.7 8.4 - - - +
81A LYS* 2.9 64.0 + - + +
83A TYR* 5.8 0.2 - - - -
43P THR* 2.5 51.1 + - + +
44P THR* 4.2 7.3 - - + +
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Residues in contact with VAL 61 (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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60A GLU* 1.3 87.7 - - - +
62A GLU* 1.3 62.9 + - - +
63A LYS 4.0 8.7 - - - +
78A VAL* 3.6 22.2 - - + -
79A ARG 4.2 2.2 - - - -
80A TRP* 3.6 25.6 - - + -
96A LEU* 4.9 8.1 - - + -
99A CYS* 4.5 5.6 - - - -
102A VAL* 4.2 29.3 - - + +
43P THR* 3.1 17.0 + - - +
44P THR 4.1 0.9 - - - -
45P ALA* 3.7 29.2 - - + +
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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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60A GLU* 4.8 0.4 - - - -
61A VAL* 1.3 76.7 - - - +
63A LYS* 1.3 94.3 + - + +
79A ARG* 3.0 33.7 + - + +
80A TRP 4.7 0.5 - - - +
81A LYS* 3.7 28.6 - - + +
82A GLY 5.2 1.6 + - - -
83A TYR 5.5 0.7 - - - +
102A VAL* 4.6 7.7 - - - +
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Residues in contact with LYS 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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61A VAL* 3.7 3.2 - - - +
62A GLU* 1.3 112.8 + - - +
64A ILE* 1.3 69.6 + - - +
65A LEU* 4.1 16.2 - - - -
78A VAL* 3.8 2.9 - - - +
79A ARG* 2.9 54.3 + - + +
102A VAL* 3.9 12.8 - - + -
105A GLU* 6.1 6.5 - - + -
109A LYS* 5.9 3.6 - - - +
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Residues in contact with ILE 64 (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 LYS* 1.3 83.4 - - - +
65A LEU* 1.3 63.1 + - - +
66A ASP 3.5 20.4 - - - +
76A TYR* 3.8 22.2 - - + -
77A LYS 3.4 7.4 - - - +
78A VAL* 4.9 0.9 - - + -
96A LEU* 3.6 34.8 - - + -
102A VAL* 3.7 19.1 + - + +
103A LEU* 3.7 31.2 - - + -
106A PHE* 3.5 38.5 - - + +
109A LYS* 4.7 5.5 + - - +
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Residues in contact with LEU 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 LYS* 4.1 23.6 - - - -
64A ILE* 1.3 75.3 - - - +
66A ASP* 1.3 75.3 + - + +
77A LYS* 2.8 33.7 + - + +
79A ARG* 3.5 38.6 - - + +
88A ASP* 3.2 41.3 - - + +
106A PHE* 3.8 3.4 - - - -
109A LYS* 3.3 22.7 + - - +
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Residues in contact with ASP 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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64A ILE* 3.5 9.2 - - - +
65A LEU* 1.3 90.0 - - - +
67A MET* 1.3 66.0 + - - +
76A TYR* 3.5 1.2 - - - -
77A LYS* 2.9 41.2 + - - +
90A TRP* 4.3 12.1 - - + -
106A PHE* 3.6 16.4 - - - -
109A LYS* 4.7 4.6 + - - -
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Residues in contact with MET 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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66A ASP* 1.3 78.4 + - - +
68A LYS* 1.3 68.6 + - - +
69A THR* 5.4 5.8 - - + -
74A VAL* 3.8 29.8 - - + -
75A LEU 3.3 11.9 - - - +
76A TYR* 3.7 20.9 - - + +
90A TRP* 3.8 7.8 - - - -
106A PHE* 3.8 20.2 - - + -
110A ILE* 5.2 11.2 - - + -
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Residues in contact with LYS 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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67A MET* 1.3 81.9 - - - +
69A THR* 1.3 71.4 + - - +
70A GLU* 3.8 32.5 + - + +
74A VAL* 3.7 2.9 - - - +
75A LEU* 2.9 40.1 + - + -
90A TRP* 3.6 56.1 - - + +
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Residues in contact with THR 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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67A MET* 5.4 5.4 - - + -
68A LYS* 1.3 83.9 - - - +
70A GLU* 1.3 65.3 + - - +
71A GLY 3.7 14.4 + - - -
72A GLY* 4.9 3.6 - - - +
73A LYS 3.0 15.0 - - - +
74A VAL* 4.3 17.3 - - + -
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Residues in contact with GLU 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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68A LYS* 3.8 28.0 + - + +
69A THR* 1.3 73.5 - - - +
71A GLY* 1.3 58.1 + - - +
72A GLY 3.4 5.5 + - - -
73A LYS* 3.0 20.9 + - + +
75A LEU* 3.6 28.3 - - + +
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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