Contacts of the strand formed by residues 73 - 80 (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 LYS 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR* 3.0 7.6 - - - -
70A GLU* 3.0 34.5 + - + +
71A GLY 3.7 0.2 - - - -
72A GLY* 1.3 80.2 - - - +
74A VAL* 1.3 66.4 + - - +
75A LEU* 3.5 23.9 - - + +
92A PRO* 3.4 39.9 - - - +
93A GLU 5.0 0.4 - - - +
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Residues in contact with VAL 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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67A MET* 3.8 28.5 - - + -
68A LYS 3.7 4.3 - - - +
69A THR* 4.3 12.6 - - + -
72A GLY 4.9 4.9 - - - +
73A LYS* 1.3 83.0 - - - +
75A LEU* 1.3 70.2 + - - +
76A TYR* 4.2 15.5 - - + +
92A PRO* 3.9 0.3 - - - +
93A GLU* 3.1 58.5 + - + +
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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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67A MET* 3.3 8.0 - - - +
68A LYS* 2.9 40.0 + - + +
70A GLU* 3.6 40.6 - - + +
73A LYS* 3.5 43.1 - - + +
74A VAL* 1.3 78.0 - - - +
76A TYR* 1.3 64.3 + - - +
90A TRP* 3.8 31.8 - - + +
91A GLU 3.3 14.4 - - - +
92A PRO* 4.9 0.7 - - + -
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Residues in contact with TYR 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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64A ILE* 3.8 28.7 - - + -
66A ASP 3.5 2.0 - - - +
67A MET* 3.7 35.5 - - + +
74A VAL* 4.2 9.0 - - + +
75A LEU* 1.3 74.9 - - - +
77A LYS* 1.3 62.3 + - - +
78A VAL* 3.5 4.3 + - - +
89A THR 3.4 1.2 - - - +
90A TRP* 3.6 4.3 - - - -
91A GLU 2.8 34.5 + - - +
93A GLU* 4.1 39.2 + - + -
96A LEU* 4.1 30.7 - - + -
103A LEU* 3.8 25.9 - - + +
106A PHE* 4.2 16.2 - + - -
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Residues in contact with LYS 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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64A ILE* 3.4 5.7 - - - +
65A LEU* 2.8 49.2 + - + -
66A ASP* 2.9 32.1 + - - +
76A TYR* 1.3 71.8 - - - +
78A VAL* 1.3 61.1 + - - +
88A ASP* 4.2 22.2 - - + -
89A THR 3.4 10.5 - - - +
90A TRP* 3.5 45.1 - - + +
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Residues in contact with VAL 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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61A VAL* 3.6 29.8 - - + -
63A LYS 3.8 3.1 - - - +
64A ILE* 4.9 1.3 - - + -
65A LEU* 4.3 2.2 - - - -
76A TYR* 3.6 12.8 - - + +
77A LYS* 1.3 78.5 - - - +
79A ARG* 1.3 65.3 + - - +
80A TRP* 3.6 37.7 + - + -
88A ASP* 3.2 26.7 - - - -
89A THR 2.9 14.1 + - - +
91A GLU* 3.9 15.0 - - + -
96A LEU* 3.7 26.0 - - + -
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Residues in contact with ARG 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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62A GLU* 3.0 51.1 + - - +
63A LYS* 2.9 35.8 + - + +
65A LEU* 3.5 27.6 - - + +
77A LYS 4.2 0.6 + - - -
78A VAL* 1.3 73.8 - - - +
80A TRP* 1.3 61.2 + - - +
83A TYR 3.9 20.2 - - - -
84A THR 4.5 2.2 - - - -
85A SER* 3.3 21.8 - - - +
88A ASP* 2.6 39.1 + - - +
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Residues in contact with TRP 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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59A PHE* 3.7 22.2 - - + -
60A GLU 3.7 14.1 - - - +
61A VAL* 3.6 24.9 - - + -
62A GLU* 4.3 1.8 - - - +
78A VAL* 3.6 29.4 + - + -
79A ARG* 1.3 77.1 - - - +
81A LYS* 1.3 66.5 + - - +
82A GLY 3.2 0.3 + - - -
83A TYR* 3.0 46.4 + - + +
84A THR 5.8 0.2 + - - -
87A ASP* 3.2 25.3 + - + -
88A ASP* 4.6 0.6 + - - -
89A THR* 3.0 29.0 + - - -
91A GLU* 3.7 9.6 - - + -
96A LEU* 6.6 0.2 - - + -
45P ALA* 3.7 17.3 - - + -
46P ARG 3.9 19.1 - - - -
47P MLY 3.6 36.2 - - + -
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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