Contacts of the strand formed by residues 59 - 64 (chain A) in PDB entry 5VFC
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 TRP 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.4 9.2 - - - +
54A SER* 2.8 34.9 + - - +
56A ASN* 4.2 9.0 - - - +
57A GLY 3.5 0.4 - - - -
58A GLU* 1.3 108.6 + - + +
60A LEU* 1.3 61.1 + - - +
71A ILE* 4.0 17.3 - - + -
72A TRP 3.3 22.0 - - - +
73A GLY* 4.1 10.1 - - - -
74A ALA* 4.0 6.0 - - - +
78A LYS 5.5 0.2 - - - -
80A GLU* 3.7 40.8 - - + -
95A TRP* 3.7 28.7 - + + -
99A SER 5.5 2.5 - - - -
116A VAL* 5.5 5.5 - - + +
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Residues in contact with LEU 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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41A LEU* 4.1 15.0 - - + -
51A VAL* 4.1 7.0 - - + -
52A LYS 3.5 29.8 - - - +
53A PHE* 3.7 19.7 - - + -
59A TRP* 1.3 73.9 - - - +
61A ALA* 1.3 64.2 + - - +
71A ILE* 3.4 4.5 - - - +
72A TRP* 2.8 45.6 + - + +
73A GLY 5.2 0.4 - - - +
74A ALA* 4.4 4.5 - - - +
95A TRP* 4.2 2.7 - - - -
308A ALA* 4.9 0.2 - - + -
317A ALA* 3.6 25.8 - - + -
327A ILE* 3.6 31.6 - - + -
329A LEU* 4.1 5.6 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER 3.9 0.2 - - - +
51A VAL* 3.2 5.7 - - - +
52A LYS 2.9 31.7 + - - +
60A LEU* 1.3 73.5 - - - +
62A SER* 1.3 60.8 + - - +
69A ILE* 4.6 1.1 - - + -
70A LYS 3.4 4.9 - - - -
71A ILE* 3.9 12.6 - - + -
93A VAL* 4.2 13.7 - - + +
95A TRP* 3.6 29.7 - - + +
102A LEU* 3.9 14.1 - - + -
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS* 2.7 27.1 + - - -
48A VAL* 4.3 2.5 - - - -
50A SER 3.3 5.8 - - - -
51A VAL* 3.8 10.3 - - - -
61A ALA* 1.3 75.0 - - - +
63A SER* 1.3 59.9 + - - +
69A ILE* 3.1 6.8 - - - +
70A LYS 2.9 31.8 + - - -
72A TRP* 2.9 19.9 + - - -
93A VAL* 4.4 3.1 - - - -
327A ILE* 3.5 23.3 - - - -
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS* 4.3 0.4 - - - -
48A VAL* 3.3 10.0 - - - +
49A SER* 2.9 39.3 + - - -
50A SER* 2.9 24.6 + - - -
62A SER* 1.3 74.0 - - - +
64A SER* 1.3 61.9 + - - +
68A LEU 3.5 6.1 - - - -
69A ILE* 4.5 3.6 - - - +
90A ILE* 3.5 26.9 - - - -
92A ASP 3.8 6.2 - - - -
93A VAL* 3.9 13.1 - - - +
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS* 3.2 19.7 + - - -
46A LYS 3.1 11.3 + - - -
47A ALA 2.8 21.4 + - - -
48A VAL* 4.2 1.1 - - - -
49A SER* 3.7 3.1 + - - -
63A SER* 1.3 79.6 - - - +
65A ALA* 1.3 61.0 + - - +
66A ASP* 3.0 33.1 + - - -
67A LYS* 3.2 8.0 + - - -
68A LEU 3.2 5.5 + - - -
90A ILE* 3.1 26.0 + - - +
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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
------------------------------------------------------------
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