Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 3DZ8
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 GLY 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS 3.5 3.5 + - - +
25A LEU* 3.4 9.5 - - - +
26A LEU* 2.9 23.9 + - - +
95A ALA* 3.6 1.5 - - - +
96A MET* 1.3 82.8 + - - +
98A PHE* 1.3 69.2 + - - -
129A GLN 3.1 12.6 - - - -
179A LEU* 3.8 17.7 - - - -
183A ILE* 4.1 0.4 - - - -
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Residues in contact with PHE 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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26A LEU* 3.2 39.0 - - + +
28A ILE* 3.9 10.5 - - + -
92A TYR* 3.7 10.8 - + - -
95A ALA* 3.4 16.8 - - + -
97A GLY* 1.3 76.4 - - - -
99A ILE* 1.3 64.3 + - - +
100A LEU* 3.8 0.7 - - + +
120A ILE* 3.1 51.6 - - + -
124A SER* 2.9 34.8 - - - -
128A ALA* 4.0 8.5 - - + -
129A GLN 2.8 9.0 + - - +
130A VAL* 3.4 17.1 - - + -
131A ILE 2.9 26.2 + - - -
179A LEU* 3.8 11.1 - - - +
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Residues in contact with ILE 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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26A LEU 2.8 9.1 + - - +
27A ILE* 3.3 10.8 - - + +
28A ILE* 2.9 30.3 + - - +
38A PHE* 4.5 5.6 - - + -
98A PHE* 1.3 73.7 - - - +
100A LEU* 1.3 62.2 + - - +
101A MET* 4.0 25.4 - - + -
131A ILE* 3.5 24.9 - - + -
133A VAL* 3.7 22.7 - - + -
175A ALA* 3.9 31.2 - - + +
176A PHE* 3.7 29.4 - - + -
179A LEU* 4.0 9.1 - - + +
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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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28A ILE* 3.6 13.7 - - + +
98A PHE* 3.8 2.1 - - + -
99A ILE* 1.3 70.9 - - - +
101A MET* 1.3 65.4 + - - +
113A VAL* 4.0 21.1 - - + +
116A TRP* 3.9 36.6 - - + +
117A ALA* 4.0 12.6 - - - +
120A ILE* 4.8 4.3 - - + -
130A VAL* 3.9 16.6 - - + -
131A ILE 2.8 9.9 + - - +
132A LEU* 3.3 21.0 - - + +
133A VAL 2.9 24.9 + - - -
159A PHE* 3.8 28.3 - - + -
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Residues in contact with MET 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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27A ILE* 3.7 21.5 - - + -
28A ILE 2.8 17.0 + - - +
29A GLY* 3.4 19.4 - - - -
30A ASN 4.1 2.4 + - - -
33A VAL* 3.7 15.6 - - + +
34A GLY 3.6 25.8 - - - +
35A LYS* 3.7 5.4 - - + -
38A PHE* 3.6 37.2 - - + -
99A ILE* 4.0 11.0 - - + -
100A LEU* 1.3 80.4 - - - +
102A TYR* 1.3 74.8 + - - +
109A SER 5.0 2.1 - - - +
113A VAL* 5.4 0.2 - - - +
116A TRP* 5.3 1.0 - - - -
133A VAL* 3.4 10.5 - - + +
135A ASN* 3.6 20.9 - - + -
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Residues in contact with TYR 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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33A VAL* 4.0 8.7 - - - -
101A MET* 1.3 75.3 - - - +
103A ASP* 1.3 66.9 + - - +
104A ILE* 4.2 8.5 - - + +
109A SER* 3.5 25.4 - - - +
110A PHE* 3.8 34.5 - + + -
113A VAL* 4.3 3.1 - - + -
132A LEU* 3.8 31.4 - - + -
133A VAL 2.9 11.9 + - - +
134A GLY* 3.5 25.8 - - - -
135A ASN* 2.7 35.2 + - - +
145A VAL* 3.9 19.3 + - + +
146A PRO 4.9 1.6 + - - -
150A GLY* 3.6 9.0 + - - -
161A PHE* 3.3 25.4 - + - -
163A GLU* 4.5 5.9 + - - -
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Residues in contact with ASP 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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32A SER 4.2 2.3 - - - +
33A VAL* 4.0 18.2 - - + -
102A TYR* 1.3 80.1 - - - +
104A ILE* 1.3 58.4 + - - +
105A THR* 2.5 37.5 + - - -
106A ASN* 2.8 43.0 + - + +
109A SER* 2.9 12.4 + - - +
135A ASN 3.6 4.7 - - - -
136A LYS* 3.0 41.2 + - - +
145A VAL* 4.2 0.7 - - - +
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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