Contacts of the strand formed by residues 98 - 103 (chain A) in PDB entry 5VLR
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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASP* 3.4 28.7 - - + +
25A LEU* 4.5 13.0 - - + -
71A THR 3.9 1.2 - - - +
72A CYS* 3.8 16.0 - - - +
73A ILE 5.0 0.9 + - - -
94A PRO* 4.9 0.8 - - - +
96A LEU* 2.9 26.6 + - + +
97A PRO* 1.3 72.1 - - - +
99A LEU* 1.3 77.0 + - - +
100A ARG* 5.6 0.4 - - + -
490B THR* 4.4 10.5 - - + -
493B ILE* 4.5 10.3 - - + -
494B PHE* 3.5 35.4 - - + -
534B ARG* 4.8 2.7 - - - +
538B ILE* 4.8 0.4 - - + -
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Residues in contact with LEU 99 (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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22A VAL* 4.0 12.3 - - + -
23A ASP 2.9 10.4 + - - +
24A PHE* 3.3 25.8 - - + -
25A LEU* 3.0 25.6 + - - +
42A LEU* 5.0 7.6 - - + -
45A ILE* 4.2 11.2 - - + -
70A PHE* 3.6 35.2 - - + -
71A THR 3.4 4.9 - - - +
72A CYS* 3.8 19.3 - - + -
82A LEU* 4.0 16.2 - - + -
89A LEU* 5.4 11.4 - - + -
92A VAL* 5.7 0.4 - - + -
94A PRO* 5.2 9.4 - - + -
98A VAL* 1.3 84.7 - - - +
100A ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.6 28.5 - - + +
69A VAL 3.3 3.8 - - - +
70A PHE* 3.4 1.9 - - - -
71A THR* 2.8 49.8 + - + +
98A VAL* 5.6 0.9 - - + -
99A LEU* 1.3 74.6 - - - +
101A LEU* 1.3 71.9 + - - +
102A VAL* 4.0 13.2 - - + -
493B ILE* 5.0 14.1 - - + +
497B GLN* 5.5 2.9 - - - +
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Residues in contact with LEU 101 (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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24A PHE* 6.4 0.2 - - + -
25A LEU 3.1 8.8 + - - +
26A LEU* 3.5 31.8 - - + -
27A PRO* 4.0 33.5 - - + +
46A LYS* 4.7 4.9 - - + -
49A LEU* 3.7 5.8 - - + -
50A TRP* 3.7 32.5 - - + -
62A LEU* 5.6 0.9 - - + -
68A TYR* 4.0 26.2 - - + -
69A VAL 3.5 5.4 - - - +
70A PHE* 3.6 31.4 - - + -
99A LEU 6.0 0.2 - - - -
100A ARG* 1.3 78.3 - - - +
102A VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 102 (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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27A PRO* 6.1 0.4 - - - -
68A TYR* 3.5 8.7 - - - -
69A VAL* 3.0 35.2 + - + +
71A THR* 3.9 23.3 - - + +
79A GLN* 6.1 0.2 - - - +
81A GLU* 4.5 14.1 - - - +
100A ARG* 4.0 16.2 - - + -
101A LEU* 1.3 80.0 - - - +
103A ALA* 1.3 78.0 + - + +
104A ARG 3.3 0.2 + - - -
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Residues in contact with ALA 103 (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 ALA 4.0 7.9 - - - +
68A TYR* 4.4 8.7 - - + -
69A VAL* 4.6 1.0 - - - +
81A GLU* 4.8 2.1 - - - +
102A VAL* 1.3 85.7 - - + +
104A ARG* 1.4 65.5 + - - +
105A GLU* 3.5 14.6 + - + +
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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