Contacts of the strand formed by residues 61 - 70 (chain B) in PDB entry 3VKO
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 ASP 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B GLN* 3.4 4.9 - - - +
52B ASN* 3.0 46.0 + - + -
59B ARG 4.6 1.6 - - - +
60B ALA* 1.3 77.0 - - - +
62B VAL* 1.3 57.8 + - - +
63B ALA 3.8 0.4 - - - -
81B LEU* 3.0 14.1 - - - +
82B ILE* 3.3 9.3 - - - +
83B ASN* 2.6 39.5 + - - +
84B GLU 4.3 0.7 + - - -
130B ILE* 3.9 19.5 - - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 3.6 35.9 - - + +
50B LEU 3.7 4.3 - - - +
51B GLN* 4.2 14.4 - - + +
59B ARG* 4.5 9.0 - - - +
60B ALA 3.8 4.0 - - - +
61B ASP* 1.3 73.7 - - - +
63B ALA* 1.3 63.8 + - - +
64B PHE 3.7 19.3 - - - +
65B HIS* 3.8 10.1 - - + +
80B THR* 3.1 4.6 - - - +
81B LEU* 2.7 60.4 + - + +
86B TRP* 4.5 1.8 - - + -
130B ILE* 4.6 0.4 - - - -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU 2.9 7.4 + - - +
51B GLN* 4.6 0.9 - - - +
52B ASN* 5.2 2.0 - - + +
61B ASP 3.8 3.4 + - - -
62B VAL* 1.3 73.3 - - - +
64B PHE* 1.3 61.2 + - - +
80B THR* 3.2 20.2 + - - +
114B PHE* 4.7 4.6 - - + -
126B TYR* 4.0 6.8 - - - -
128B HIS* 6.0 0.2 - - - -
129B ARG* 5.0 4.9 + - - +
130B ILE* 4.0 37.3 - - + +
135B ILE* 3.6 36.1 - - + -
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL 3.3 4.3 - - - +
49B ASP* 3.3 5.4 - - - -
50B LEU* 3.0 51.7 + - + -
62B VAL* 3.1 3.7 - - - -
63B ALA* 1.3 82.6 - - - +
65B HIS* 1.3 65.8 + - - +
66B PHE* 3.9 26.0 - + + -
78B CYS* 3.8 18.8 - - + -
79B ASN 3.9 0.7 - - - -
107B ILE* 4.3 13.2 - - + -
114B PHE* 3.6 32.1 - + + -
116B VAL* 4.1 24.0 - - + -
124B LEU* 4.4 0.7 - - + -
126B TYR* 3.5 42.8 - + + -
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 3.7 0.2 + - - -
47B GLN* 3.0 45.5 - - + +
49B ASP* 2.5 27.1 + - - -
62B VAL* 3.8 2.9 - - + +
64B PHE* 1.3 73.6 - - - +
66B PHE* 1.3 56.4 + - - +
67B ASN* 3.4 18.6 - - + +
77B VAL* 3.3 3.8 - - + +
78B CYS* 3.1 27.9 - - - +
79B ASN* 2.8 24.6 + - + +
86B TRP* 3.2 34.9 - + + -
2D GAL 2.8 35.1 + - - -
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 4.3 0.9 - - - -
48B VAL* 2.9 54.6 + - + +
64B PHE* 3.7 28.6 + + + -
65B HIS* 1.3 70.4 - - - +
67B ASN* 1.3 58.7 + - - +
68B PRO* 3.2 19.2 - - + +
76B ILE* 3.8 10.3 - - + -
77B VAL 4.0 0.4 - - - -
78B CYS* 4.1 7.0 - - - -
97B PHE* 3.5 40.8 - + - -
105B ILE* 3.8 19.5 - - + -
107B ILE* 5.4 2.7 - - + -
116B VAL* 3.8 26.0 - - + -
118B VAL* 4.9 2.9 - - + -
123B THR* 5.1 0.9 - - + -
124B LEU* 3.7 25.4 - - + -
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 3.1 34.9 + - - +
46B PHE 2.8 27.2 + - - -
47B GLN* 4.3 0.4 - - - -
65B HIS* 3.4 21.1 - - + +
66B PHE* 1.3 71.4 - - - +
68B PRO* 1.3 67.3 + - - +
69B ARG* 2.7 35.5 + - - +
76B ILE* 3.5 2.5 - - - +
77B VAL* 2.7 47.8 + - + +
2D GAL 3.5 1.0 + - - -
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Residues in contact with PRO 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 3.4 23.0 - - - +
46B PHE* 3.0 55.4 + - + +
66B PHE* 3.2 19.7 - - + +
67B ASN* 1.3 82.5 - - - +
69B ARG* 1.3 60.8 + - - +
70B PHE* 3.9 9.4 - - + -
75B CYS 3.6 6.5 - - - +
76B ILE* 4.2 4.7 - - + -
95B THR* 5.4 0.4 - - - +
97B PHE* 3.8 34.5 - - + -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP 3.9 5.6 - - - +
45B ARG* 3.3 22.3 - - + +
67B ASN* 2.7 25.4 + - - +
68B PRO* 1.3 78.3 - - - +
70B PHE* 1.3 69.4 + - - +
71B LYS* 4.8 26.6 - - + +
74B GLY* 3.5 1.4 - - - -
75B CYS* 2.7 45.2 + - - +
77B VAL* 3.6 23.1 - - + +
89B GLU* 4.0 3.0 + - - -
95B THR* 5.2 1.9 + - - +
1D NAG 3.1 34.9 + - - +
2D GAL 3.2 40.4 + - - -
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.4 33.2 - - + -
43B ALA* 3.8 13.0 - - + +
44B ASP 3.3 24.0 + - - +
45B ARG* 4.0 8.1 - - - -
46B PHE* 4.0 17.5 - + - -
68B PRO* 3.9 17.5 - - + -
69B ARG* 1.3 79.5 - - - +
71B LYS* 1.3 71.1 + - - +
72B ARG 2.9 14.4 + - - +
74B GLY* 3.8 5.9 - - - -
95B THR* 5.5 1.6 - - + -
97B PHE* 3.6 29.2 - - + -
98B LYS* 4.0 11.2 - - - -
99B ARG* 3.4 40.3 + - + +
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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