Contacts of the strand formed by residues 32 - 37 (chain A) in PDB entry 2XN9
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 5.2 5.8 - - + -
23A CYS* 4.5 4.3 - - - -
29A PHE* 4.9 13.0 - - + -
31A SER* 1.3 76.3 - - - +
33A GLN* 1.3 67.9 + - - +
34A TRP* 3.9 9.6 - - + +
47A VAL* 5.4 0.5 - - - +
48A THR* 3.4 1.7 - - - -
49A VAL* 2.8 47.2 + - + +
65A PHE* 3.9 21.5 - - + -
70A LYS 5.6 1.3 - - - -
71A ASP* 4.4 4.7 - - - +
72A SER* 3.3 43.1 - - - +
89A CYS* 3.9 23.3 - - - -
90A ALA 3.3 10.3 - - - +
91A GLY* 4.9 0.9 - - - -
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Residues in contact with GLN 33 (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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31A SER* 5.4 3.1 - - - +
32A LEU* 1.3 79.6 - - - +
34A TRP* 1.3 66.9 + - - +
35A TYR* 2.9 34.4 + - + -
45A LEU* 3.6 9.6 - - + +
47A VAL 3.5 5.2 - - - +
48A THR* 2.8 34.5 + - + +
88A LEU 4.5 0.2 - - - -
89A CYS* 3.3 7.8 - - - -
90A ALA* 2.6 40.3 + - + +
98A LEU* 3.4 26.1 - - + +
101B TYR* 3.3 34.3 + - - +
102B GLU 3.9 1.2 - - - +
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Residues in contact with TRP 34 (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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6A GLN* 3.6 23.1 - - - -
21A VAL* 4.0 26.9 - - + -
22A TYR 4.0 9.0 - - - -
23A CYS* 3.8 29.2 - - + -
32A LEU* 3.9 7.5 - - + +
33A GLN* 1.3 77.7 - - - +
35A TYR* 1.3 55.8 + - - +
45A LEU* 3.7 4.2 - - - +
46A LEU* 2.8 33.7 + - + +
47A VAL* 3.1 15.8 + - + -
49A VAL* 5.7 1.8 - - + -
63A PHE* 3.6 33.4 - + + -
72A SER* 3.1 35.6 + - - -
73A SER 4.1 4.4 + - - -
74A LEU* 3.8 30.7 - - + -
87A TYR* 4.4 9.0 - - + -
88A LEU 3.4 16.6 - - - -
89A CYS* 4.0 3.6 - - + -
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLN* 2.9 37.4 + - + -
34A TRP* 1.3 76.3 - - - +
36A ARG* 1.3 59.1 + - - +
43A PRO* 3.9 24.5 - - + -
44A VAL 3.2 8.7 - - - +
45A LEU* 3.3 38.5 - - + +
46A LEU* 4.2 4.9 - - - +
87A TYR* 3.4 7.3 - - - +
88A LEU* 2.7 48.2 + - + +
90A ALA* 4.1 10.3 - - + -
98A LEU* 4.0 1.4 - - - +
100A PHE* 3.9 17.5 - + - -
103B GLN* 3.3 44.5 + - - +
105B PHE* 3.8 13.0 - + - -
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Residues in contact with ARG 36 (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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35A TYR* 1.3 74.1 - - - +
37A GLN* 1.3 65.2 + - - +
38A GLU* 2.7 38.9 + - - +
42A GLY 4.5 0.3 - - - +
43A PRO* 3.4 1.7 - - - +
44A VAL* 2.9 37.2 + - + +
46A LEU* 4.1 27.0 - - + +
82A GLY 3.0 26.2 + - - -
83A ASP* 4.6 0.4 - - - +
84A THR 3.0 21.3 + - - -
85A GLY* 5.0 2.0 - - - -
86A LEU 3.4 5.2 - - - +
87A TYR* 3.6 35.0 + - + +
88A LEU* 5.8 0.2 - - - -
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Residues in contact with GLN 37 (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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36A ARG* 1.3 79.1 - - - +
38A GLU* 1.3 75.4 + - - +
39A PRO* 4.2 1.6 - - - +
40A GLY 4.9 2.4 - - - +
41A GLU 2.7 25.4 + - - +
42A GLY 4.2 1.6 - - - -
43A PRO* 3.8 30.5 - - + +
85A GLY* 3.7 4.9 - - - -
86A LEU* 2.8 52.4 + - + +
88A LEU* 4.1 6.0 - - + +
39B GLN* 2.7 45.1 + - - -
90B PHE* 4.1 4.2 - - - -
92B LEU* 4.1 2.6 - - - +
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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