Contacts of the strand formed by residues 94 - 100 (chain A) in PDB entry 2Q2L
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 ALA 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.3 4.7 + - - -
34A ILE* 2.8 38.4 + - + +
37A LEU* 4.9 0.2 - - + -
86A ILE* 4.0 19.3 - - + -
87A THR 3.7 19.7 - - - +
88A VAL* 3.7 16.8 - - + -
93A THR* 1.3 77.9 - - - +
95A CYS* 1.3 59.2 + - - +
96A PHE* 4.2 9.6 - - + -
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Residues in contact with CYS 95 (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 GLY 3.4 7.6 - - - -
33A ASN* 3.8 15.9 - - - +
87A THR 4.9 1.4 + - - -
93A THR* 6.4 0.2 - - - -
94A ALA* 1.3 71.7 - - - +
96A PHE* 1.3 63.5 + - - +
140B GLY* 3.7 13.9 - - - -
141B GLY* 3.6 33.0 - - - +
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Residues in contact with PHE 96 (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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18A ILE* 4.1 3.1 - - + -
30A VAL* 4.2 7.4 - - + -
31A THR* 3.2 4.3 + - - -
32A GLY* 2.7 69.5 + - - +
34A ILE* 3.9 18.2 - - + -
44A PHE* 3.8 38.1 - + - -
86A ILE* 3.7 42.6 - - + -
87A THR 5.9 0.9 - - - +
94A ALA* 4.2 3.4 - - + -
95A CYS* 1.3 85.2 - - - +
97A THR* 1.3 64.4 + - - +
98A ILE* 3.9 16.6 - - + -
2005A IOD 3.9 13.5 - - + -
132B LEU* 5.7 0.2 - - - -
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Residues in contact with THR 97 (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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29A THR* 3.9 22.7 - - + -
30A VAL 2.9 11.9 - - - +
31A THR* 3.8 11.0 - - - -
96A PHE* 1.3 72.9 + - - +
98A ILE* 1.3 70.1 + - - +
99A VAL* 4.3 12.1 - - + -
2005A IOD 3.6 15.5 - - - +
131B GLU* 6.6 0.4 - - + -
132B LEU* 3.6 41.1 - - + +
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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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29A THR* 3.6 1.4 - - - -
30A VAL* 2.8 40.8 + - + +
44A PHE* 4.1 17.3 - - + -
73A PRO* 5.8 4.9 - - + -
83A LEU* 3.9 39.9 - - + +
85A ASN 5.0 3.8 - - - +
86A ILE* 4.3 7.9 - - + -
96A PHE* 3.9 27.8 - - + -
97A THR* 1.3 79.9 - - - +
99A VAL* 1.3 71.9 + - - +
100A ASP* 4.4 8.1 - - + +
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Residues in contact with VAL 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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27A PRO* 3.5 32.1 - - + -
28A THR 3.4 4.7 - - - +
29A THR* 3.9 18.2 - - + +
97A THR* 4.3 15.0 - - + -
98A ILE* 1.3 79.8 - - - +
100A ASP* 1.3 67.7 + - - +
101A LYS* 3.7 17.9 - - - +
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Residues in contact with ASP 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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27A PRO* 3.4 0.5 - - - +
28A THR* 2.8 35.5 + - - +
73A PRO* 4.3 8.8 - - - +
78A ARG* 3.0 43.5 + - - -
80A ALA 4.0 0.3 - - - +
83A LEU* 3.8 15.7 - - + +
98A ILE* 4.4 7.4 - - + -
99A VAL* 1.3 78.0 - - - +
101A LYS* 1.3 72.1 + - - +
102A GLN* 3.3 13.7 + - - +
103A ILE* 3.7 24.9 + - + +
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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