Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 3F3Z
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LYS* 3.5 36.1 + - + +
59A ILE 3.4 5.6 - - - +
60A PRO* 3.3 26.7 - - - +
61A LYS* 4.1 2.6 - - - +
93A GLU* 3.6 1.9 - - - -
94A ASP* 2.7 44.4 + - - +
95A ASN 3.8 0.4 - - - -
96A THR* 1.3 96.6 + - - +
98A ILE* 1.3 66.1 + - - +
99A TYR* 3.9 21.4 + - + -
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Residues in contact with ILE 98 (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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57A LYS 3.4 2.4 - - - +
58A LYS* 3.6 1.7 - - - -
59A ILE* 2.8 47.0 + - + +
61A LYS* 3.7 32.1 - - + -
64A VAL* 4.4 14.1 - - + -
70A PHE* 3.6 32.3 - - + -
91A THR* 5.0 4.7 - - - -
92A PHE 3.6 11.0 - - - +
93A GLU* 4.2 13.5 - - + +
97A ASP* 1.3 76.4 - - - +
99A TYR* 1.3 65.7 + - - +
100A LEU* 3.8 23.3 - - + -
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Residues in contact with TYR 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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24A ILE* 3.7 47.2 - - + +
25A ASN* 5.5 1.9 + - - -
30A LEU* 3.8 22.6 - - + +
43A LYS* 5.0 0.4 - - - -
56A ALA* 4.7 7.9 - - + -
57A LYS 3.3 4.5 - - - -
58A LYS* 3.4 54.9 + - + +
91A THR* 3.2 10.4 - - - -
92A PHE* 2.9 45.4 + - + +
93A GLU 4.9 1.1 - - - -
94A ASP* 3.9 18.4 + - - -
97A ASP* 3.9 18.5 + - + -
98A ILE* 1.3 75.4 - - - +
100A LEU* 1.3 63.6 + - - +
101A VAL* 4.0 0.8 + - - -
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Residues in contact with LEU 100 (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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55A ALA 3.4 2.1 - - - +
56A ALA* 3.3 2.7 - - - -
57A LYS* 2.8 40.5 + - + +
59A ILE* 4.0 23.6 - - + -
70A PHE* 4.3 4.3 - - + -
73A GLU* 5.3 3.4 - - - +
74A ILE* 3.6 33.2 - - + -
77A MET* 4.7 12.3 - - - -
88A LEU* 3.8 12.1 - - + -
90A GLU 4.0 3.4 - - - -
91A THR* 3.7 22.2 - - + -
98A ILE* 3.8 17.5 - - + -
99A TYR* 1.3 75.3 - - - +
101A VAL* 1.3 62.6 + - - +
102A MET* 3.6 21.4 - - + +
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Residues in contact with VAL 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 ILE* 3.9 28.9 - - + -
28A TYR* 3.5 31.2 - - + +
45A ALA* 5.2 1.3 - - + -
54A ARG* 3.8 25.4 - - + +
55A ALA 3.5 4.9 - - - +
56A ALA* 4.5 5.2 - - + -
88A LEU* 3.5 3.8 - - - +
89A TYR* 2.8 34.5 + - + +
90A GLU* 2.9 23.6 + - + +
92A PHE* 4.1 16.8 - - + -
99A TYR 4.9 0.9 - - - +
100A LEU* 1.3 73.6 - - - +
102A MET* 1.3 56.0 + - - +
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Residues in contact with MET 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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1A DRK 3.3 45.8 - - + -
42A VAL* 5.9 0.4 - - + -
54A ARG* 3.3 7.8 - - - +
55A ALA 2.7 33.9 + - - +
57A LYS* 3.5 34.3 - - + +
77A MET* 4.0 23.3 - - - +
86A ILE* 4.3 6.1 - - + -
87A ARG 3.2 14.1 - - - +
88A LEU* 3.7 15.9 - - + -
89A TYR* 3.7 6.7 - - - -
100A LEU* 3.6 20.4 - - + +
101A VAL* 1.3 79.4 - - - +
103A GLU* 1.3 60.0 - - - +
168A ILE 4.8 1.1 - - - +
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Residues in contact with GLU 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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1A DRK 2.9 24.3 + - - -
54A ARG* 5.2 0.7 - - - +
55A ALA 4.3 0.2 - - - -
86A ILE* 3.6 16.7 - - + +
87A ARG* 2.8 38.8 + - + +
89A TYR* 3.4 30.0 + - + +
102A MET* 1.3 74.7 - - - +
104A LEU* 1.3 63.3 - - - +
157A LEU* 4.0 13.2 - - + +
166A LYS* 2.8 41.3 + - - -
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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