Contacts of the strand formed by residues 63 - 70 (chain A) in PDB entry 2X2P
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 LEU 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.5 36.9 - - + +
38A LEU* 3.8 14.8 - - + +
56A LEU* 3.9 18.6 - - + -
60A ASN* 3.2 18.6 + - + +
61A GLU 4.7 0.2 - - - +
62A LYS* 1.3 73.2 - - - +
64A LYS* 1.3 73.6 + - - +
65A GLY 3.4 28.3 - - - +
66A VAL* 5.3 0.7 - - + -
85A ILE* 4.1 10.8 - - + -
89A TYR* 4.1 21.1 - - + -
91A VAL* 3.4 33.0 - - + +
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Residues in contact with LYS 64 (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 MET* 4.0 13.7 - - + -
35A ASP* 3.8 35.7 - - + +
36A PHE 2.8 12.8 + - - +
37A ILE* 4.0 4.7 - - + -
61A GLU 3.8 10.7 + - - -
62A LYS* 3.4 19.5 + - - +
63A LEU* 1.3 97.3 + - - +
65A GLY* 1.3 57.2 + - - +
91A VAL* 4.0 6.5 - - - -
92A PRO* 3.3 20.4 - - - +
116A ILE* 3.8 16.9 - - + +
117A ALA* 6.3 0.7 - - - -
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Residues in contact with GLY 65 (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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37A ILE* 3.5 17.2 - - - +
38A LEU 3.0 22.7 + - - -
63A LEU* 3.4 11.6 - - - +
64A LYS* 1.3 77.4 - - - +
66A VAL* 1.3 61.7 + - - -
91A VAL* 3.9 8.2 - - - +
92A PRO* 3.3 14.6 - - - -
94A VAL* 4.1 4.7 - - - -
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Residues in contact with VAL 66 (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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38A LEU* 3.3 17.7 - - + +
40A THR* 4.2 4.5 - - + -
63A LEU* 5.3 0.4 - - + -
65A GLY* 1.3 75.4 - - - +
67A SER* 1.3 72.7 + - - +
82A ALA* 3.8 29.8 - - + +
85A ILE* 3.9 42.0 - - + -
86A SER* 4.1 6.1 - - - +
91A VAL* 4.5 2.5 - - + -
92A PRO 3.0 11.7 + - - +
93A ILE* 3.3 9.3 - - - +
94A VAL* 2.8 32.7 + - - +
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Residues in contact with SER 67 (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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37A ILE* 4.7 0.6 - - - +
38A LEU 2.9 5.6 + - - +
39A ILE* 3.4 11.6 - - - -
40A THR* 3.1 23.0 + - - +
66A VAL* 1.3 80.0 - - - +
68A ALA* 1.3 60.5 + - - +
82A ALA* 4.5 0.9 - - - -
94A VAL* 4.5 0.4 - - - -
95A SER* 2.8 35.8 + - - -
97A PHE* 3.4 18.0 - - - -
109A PHE* 3.8 24.4 - - - -
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Residues in contact with ALA 68 (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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40A THR* 3.2 5.2 - - + +
67A SER* 1.3 74.1 + - - +
69A SER* 1.3 61.1 + - - +
79A GLY* 3.8 18.3 - - - +
81A SER* 3.4 26.5 - - - +
82A ALA* 3.7 18.2 - - + +
95A SER 3.2 6.9 + - - -
96A LYS* 3.3 6.7 - - + +
97A PHE* 3.0 31.7 + - - +
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Residues in contact with SER 69 (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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11A ASN* 4.4 0.2 - - - +
12A VAL* 3.5 28.7 - - - +
40A THR 2.9 6.8 + - - -
41A TYR* 3.4 1.1 - - - -
42A THR* 3.2 30.4 + - - -
68A ALA* 1.3 74.1 - - - +
70A GLY* 1.3 58.0 + - - +
79A GLY* 5.2 0.7 - - - -
97A PHE* 3.3 22.3 - - - -
99A LEU 2.7 23.0 + - - -
1119A FMN 2.7 23.1 + - - -
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Residues in contact with GLY 70 (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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42A THR* 4.4 0.7 - - - -
68A ALA 4.1 0.2 + - - -
69A SER* 1.3 74.1 + - - +
71A ASN* 1.3 63.6 + - - +
78A PHE* 3.8 9.8 - - - -
79A GLY* 4.6 1.1 - - - -
97A PHE 2.9 8.8 + - - -
98A GLU* 3.2 2.4 - - - +
99A LEU* 2.9 28.1 + - - +
1119A FMN 3.2 29.7 - - - -
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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