Contacts of the strand formed by residues 59 - 68 (chain A) in PDB entry 2VCK
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP* 3.4 5.4 - - - -
49A GLY 2.8 45.2 + - - +
50A GLY* 3.7 9.2 - - - +
57A GLY 4.1 1.4 - - - +
58A ASP* 1.3 79.4 + - - +
60A LYS* 1.3 65.3 + - - +
79A ILE* 5.3 0.7 - - + -
80A VAL 3.3 4.9 - - - +
81A ASP* 3.9 13.9 - - + -
211A TYR* 5.1 2.2 - - - +
215A LYS* 4.2 11.4 - - + -
216A PHE* 4.1 14.8 - - + -
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Residues in contact with LYS 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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47A TRP 3.3 3.8 - - - +
48A ASP* 3.2 31.9 - - - +
57A GLY 3.5 23.4 + - - +
58A ASP 5.0 2.2 - - - +
59A ALA* 1.3 76.2 - - - +
61A LEU* 1.3 61.1 + - - +
62A THR* 5.5 2.0 - - - +
78A HIS 3.7 1.4 - - - +
79A ILE* 3.3 5.7 - - - +
80A VAL* 2.9 40.3 + - + +
216A PHE* 4.3 2.9 - - - -
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Residues in contact with LEU 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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45A ALA* 3.8 22.2 - - + -
46A LYS* 3.2 7.1 - - - +
47A TRP* 2.9 44.6 + - + +
60A LYS* 1.3 74.4 - - - +
62A THR* 1.3 70.3 + - - +
63A ALA* 3.8 21.3 - - + +
78A HIS 3.5 3.1 - - - +
79A ILE* 3.8 18.4 - - + +
212A MSE 3.4 32.3 - - + -
216A PHE* 3.8 17.2 - - + -
224A PHE* 3.6 22.4 - - + -
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Residues in contact with THR 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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43A VAL* 5.2 0.2 - - + -
45A ALA 3.4 5.6 - - - +
46A LYS* 2.9 34.8 + - + +
60A LYS* 5.5 2.6 - - - +
61A LEU* 1.3 77.2 + - - +
63A ALA* 1.3 62.0 + - - +
64A ASN* 3.7 30.7 - - - +
76A GLU 3.7 1.0 - - - +
77A ALA* 3.4 2.8 - - - -
78A HIS* 2.9 44.4 + - + +
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Residues in contact with ALA 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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43A VAL* 3.6 1.6 - - - -
44A TRP* 2.8 43.1 + - + -
45A ALA 2.9 12.3 + - - +
61A LEU* 3.8 16.1 - - + +
62A THR* 1.3 73.5 - - - +
64A ASN* 1.3 57.7 + - - +
76A GLU 3.3 5.6 - - - -
224A PHE* 4.4 2.9 - - + -
228A PHE* 3.5 34.3 - - + -
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Residues in contact with ASN 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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40A ILE* 3.6 28.6 - - + +
42A GLU 3.6 3.8 - - - +
43A VAL* 3.7 23.4 - - - +
62A THR* 3.7 23.8 - - - +
63A ALA* 1.3 78.1 - - - +
65A ILE* 1.3 63.8 + - - +
66A ARG* 4.5 2.9 - - - +
74A ALA 3.8 0.5 - - - +
75A ARG* 3.6 1.2 - - - -
76A GLU* 2.9 62.9 + - + +
228A PHE* 3.3 6.1 - - - -
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Residues in contact with ILE 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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40A ILE* 3.5 3.8 - - - +
41A SER* 2.7 45.5 + - - +
42A GLU* 2.7 49.7 + - + +
44A TRP* 4.5 15.0 - - + -
64A ASN* 1.3 75.2 - - - +
66A ARG* 1.3 64.7 + - - +
67A THR* 4.5 3.4 - - + -
73A LYS* 4.3 24.0 - - + +
74A ALA 3.7 2.7 - - - +
75A ARG* 4.9 5.8 - - + -
227A ASP 5.9 1.8 - - - +
228A PHE* 3.8 17.0 - - + -
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Residues in contact with ARG 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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32A PHE* 3.3 41.5 - - - -
38A LEU* 3.0 28.7 + - + -
39A GLU* 3.1 19.5 - - - +
40A ILE* 3.8 30.0 - - + +
41A SER* 4.1 0.2 - - - -
64A ASN* 4.5 3.9 - - + +
65A ILE* 1.3 76.6 - - - +
67A THR* 1.3 64.7 + - - +
73A LYS* 3.3 6.9 - - - +
74A ALA* 2.7 51.5 + - + +
76A GLU* 2.9 35.6 + - - +
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Residues in contact with THR 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 GLN 3.0 14.0 - - - +
38A LEU* 3.5 7.8 - - - -
39A GLU* 3.0 17.3 + - - +
41A SER* 3.5 26.8 - - - +
65A ILE* 4.5 7.2 - - + -
66A ARG* 1.3 79.1 - - - +
68A GLY* 1.3 59.7 + - - +
71A PHE 5.0 2.2 - - - -
72A LEU 3.8 18.4 - - - +
73A LYS* 4.7 3.8 - - + +
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Residues in contact with GLY 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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37A GLN* 3.4 17.7 - - - -
38A LEU* 4.2 3.1 - - - +
67A THR* 1.3 79.4 - - - +
69A GLU* 1.3 68.9 + - - -
70A HIS 3.2 0.7 + - - -
71A PHE* 3.1 23.5 + - - +
94A LYS* 4.9 3.6 + - - -
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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