Contacts of the strand formed by residues 48 - 56 (chain B) in PDB entry 5WVD
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 TYR 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLN* 3.4 22.3 + - - +
44B PHE* 3.0 43.1 + + + +
45B GLU* 4.1 5.4 - - - +
46B ASP 3.9 0.4 - - - -
47B MET* 1.3 94.6 - - + +
49B LYS* 1.3 59.4 + - - +
66B ALA* 4.2 19.3 - - + -
67B VAL 3.5 3.1 - - - +
68B SER* 3.7 35.8 - - - -
69B LEU* 4.2 5.6 - - - -
75B TYR* 3.8 18.3 - + - -
77B VAL* 6.0 0.2 - - + -
111B ILE* 5.5 1.6 - - - +
112B GLU* 2.7 31.9 + - - +
114B PHE* 6.1 0.4 - - + -
123B VAL* 3.5 33.8 - - + +
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Residues in contact with LYS 49 (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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83A GLN* 3.7 21.0 + - + +
223A ALA* 4.3 22.4 - - + -
224A PRO* 6.2 0.2 - - + -
45B GLU 5.7 0.2 - - - -
48B TYR* 1.3 71.6 - - - +
50B LEU* 1.3 72.2 + - - +
51B THR* 4.5 1.3 - - + +
66B ALA* 3.4 1.6 - - - -
67B VAL* 2.7 49.2 + - + +
69B LEU* 4.0 25.6 - - + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 5.3 0.9 - - - +
81A GLU* 3.7 28.0 - - + +
83A GLN* 2.9 38.4 + - + +
223A ALA* 4.0 1.7 - - - -
224A PRO* 3.4 18.5 - - + +
44B PHE* 4.2 7.9 - - + -
49B LYS* 1.3 85.4 - - - +
51B THR* 1.3 59.3 + - - +
64B GLN* 3.6 39.5 - - + +
65B GLY 3.7 4.7 - - - +
66B ALA* 4.3 2.7 - - + +
77B VAL* 3.8 28.3 - - + -
79B ILE* 3.9 14.4 - - + -
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Residues in contact with THR 51 (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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221A TYR* 4.0 22.3 - - + +
222A MET 3.5 11.4 - - - +
223A ALA* 4.5 0.7 - - - +
224A PRO* 3.5 5.5 - - - +
49B LYS* 4.5 1.6 - - + +
50B LEU* 1.3 75.7 - - - +
52B SER* 1.3 57.5 + - - +
53B GLU* 3.3 16.7 + - - +
64B GLN* 2.7 28.8 + - - +
65B GLY* 2.9 33.3 + - - +
66B ALA 4.6 0.4 - - - +
67B VAL* 3.9 30.3 - - + +
74B GLU* 4.7 8.1 + - - +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 3.8 13.7 - - - +
196A SER 3.5 28.5 - - - +
197A GLY* 3.8 16.2 - - - -
221A TYR* 3.6 12.0 - - - -
222A MET* 2.8 39.0 + - - +
224A PRO* 4.0 15.7 - - - -
51B THR* 1.3 72.6 - - - +
53B GLU* 1.3 57.6 + - - +
54B LEU* 3.5 4.7 + - - +
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Residues in contact with GLU 53 (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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221A TYR* 3.7 42.1 + - + +
51B THR* 3.3 12.8 + - - +
52B SER* 1.3 75.5 - - - +
54B LEU* 1.3 61.9 + - - +
55B LEU* 3.5 29.4 + - + +
64B GLN* 3.5 5.1 - - - +
65B GLY* 3.1 28.6 + - - +
74B GLU* 3.8 7.8 - - - +
126B LYS* 2.8 35.3 + - - +
401B 7UX 3.8 14.9 + - - +
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Residues in contact with LEU 54 (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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57A GLU* 3.4 35.0 - - + +
58A GLY* 3.7 25.1 - - - +
59A ALA* 4.8 5.2 - - + +
52B SER 3.5 6.2 + - - +
53B GLU* 1.3 72.0 - - - +
55B LEU* 1.3 63.4 + - - +
56B GLY 3.6 21.5 - - - +
57B GLU* 4.5 14.6 - - + +
62B LYS* 4.0 23.8 - - + -
63B VAL 3.9 7.6 - - - +
64B GLN* 4.4 9.6 - - + +
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Residues in contact with LEU 55 (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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53B GLU* 3.5 38.3 + - + +
54B LEU* 1.3 73.7 - - - +
56B GLY* 1.3 56.7 + - - +
63B VAL* 2.8 29.7 + - + +
65B GLY* 4.2 13.2 - - - +
76B ALA* 3.9 13.9 - - + -
126B LYS* 5.0 4.0 - - + -
192B PHE* 3.9 13.2 - - + -
401B 7UX 3.8 58.2 - - + +
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Residues in contact with GLY 56 (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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54B LEU* 3.4 13.2 - - - +
55B LEU* 1.3 80.7 - - - +
57B GLU* 1.3 63.3 + - - -
62B LYS* 3.4 7.8 - - - +
63B VAL 3.1 24.1 + - - -
192B PHE* 4.4 5.2 - - - -
194B LEU* 3.6 17.0 - - - -
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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