Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 2XKL
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 GLN 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PRO* 5.0 6.1 - - - +
26A HIS* 3.7 23.2 + - - +
75A ALA* 3.7 5.5 - - - +
76A GLY* 2.8 41.6 + - - +
78A ALA* 3.4 35.4 + - - +
79A PRO 3.3 5.4 - - - +
80A ARG* 1.3 80.8 - - - +
82A LEU* 1.3 59.9 + - - +
83A GLN* 4.9 2.4 - - - +
101A THR* 4.1 17.6 + - - -
102A TYR 3.4 14.4 - - - +
103A ARG* 4.9 2.9 - - + -
104A LEU* 4.3 9.0 - - - +
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Residues in contact with LEU 82 (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 LEU* 3.9 18.2 - - + -
43A HIS* 3.5 33.2 - - + +
73A MET* 4.2 20.4 - - + -
74A ALA 3.5 11.2 - - - +
81A GLN* 1.3 77.4 - - - +
83A GLN* 1.3 61.9 + - - +
84A LEU* 3.6 26.5 - - + -
101A THR* 3.4 2.9 - - - -
102A TYR* 2.8 45.0 + - + +
104A LEU* 4.0 29.3 - - + +
136A LEU* 5.0 5.2 - - + -
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Residues in contact with GLN 83 (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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72A ASN 3.6 1.4 - - - +
73A MET* 3.5 2.8 - - - -
74A ALA* 2.8 43.0 + - + +
75A ALA 4.6 3.4 + - - -
76A GLY* 4.0 26.6 - - - +
77A SER* 6.0 1.0 - - - -
81A GLN* 4.9 2.9 - - - +
82A LEU* 1.3 78.3 - - - +
84A LEU* 1.3 62.6 + - - +
85A ARG* 3.6 36.1 + - - +
99A LYS* 3.1 28.2 + - - +
100A TRP 3.2 5.4 - - - +
101A THR* 3.6 18.8 - - - +
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Residues in contact with LEU 84 (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 LEU* 4.7 1.8 - - + -
71A PHE* 3.8 27.1 - - + -
72A ASN 3.4 3.8 - - - +
73A MET* 4.0 11.4 - - + -
82A LEU* 3.6 31.4 - - + -
83A GLN* 1.3 75.6 - - - +
85A ARG* 1.3 61.2 + - - +
86A ALA* 3.9 1.4 + - + +
98A ARG 3.7 0.9 - - - +
99A LYS* 3.3 3.7 - - - +
100A TRP* 2.8 49.5 + - + +
102A TYR* 3.9 24.0 - - + +
149A TYR* 3.8 10.5 - - + +
1191A POL 3.5 35.7 - - - +
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Residues in contact with ARG 85 (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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71A PHE* 3.1 3.9 - - - -
72A ASN* 3.0 52.7 + - - +
74A ALA* 3.9 23.6 - - - +
83A GLN* 3.6 35.2 + - - +
84A LEU* 1.3 70.7 - - - +
86A ALA* 1.3 58.0 + - - +
98A ARG 3.4 5.6 - - - +
99A LYS* 3.7 30.6 - - + +
187A LEU* 3.6 12.9 - - + +
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Residues in contact with ALA 86 (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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69A ILE* 3.8 15.3 - - + -
70A VAL 3.3 6.5 - - - +
71A PHE* 3.7 14.8 - - + -
84A LEU* 5.0 1.1 - - + +
85A ARG* 1.3 73.9 - - - +
87A THR* 1.3 67.1 + - - +
88A ILE* 5.1 0.4 - - + +
97A PRO* 3.4 2.4 - - - +
98A ARG* 2.7 46.4 + - + +
100A TRP* 4.3 17.0 - - + -
187A LEU* 3.9 5.1 - - - +
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Residues in contact with THR 87 (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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68A ASN* 5.0 0.5 - - - +
69A ILE* 3.8 1.9 - - - -
70A VAL* 2.9 35.4 + - - +
86A ALA* 1.3 76.7 + - - +
88A ILE* 1.3 64.8 + - - +
89A ARG 3.6 2.8 + - - -
95A CYS* 3.8 16.8 - - + -
96A VAL 3.6 1.6 - - - -
97A PRO* 3.8 23.9 - - + +
185A CYS* 3.4 24.7 - - + +
186A PRO* 2.6 29.0 + - + +
187A LEU* 3.7 10.8 - - - +
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Residues in contact with ILE 88 (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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66A VAL* 3.9 24.5 - - + -
68A ASN 3.7 5.8 - - - +
69A ILE* 4.0 21.3 - - + -
86A ALA* 5.1 0.4 - - + -
87A THR* 1.3 73.8 - - - +
89A ARG* 1.3 75.4 + - - +
90A THR* 3.6 9.1 + - - +
94A VAL 3.5 0.7 - - - +
95A CYS* 3.3 5.0 - - - -
96A VAL* 2.8 52.3 + - + +
98A ARG* 4.1 17.3 - - + +
100A TRP* 3.7 31.6 - - + -
185A CYS* 4.0 1.6 - - - -
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Residues in contact with ARG 89 (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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67A ASP* 2.8 30.4 + - - +
68A ASN* 2.8 44.1 + - - +
87A THR 3.6 3.2 + - - -
88A ILE* 1.3 76.8 - - - +
90A THR* 1.3 60.8 + - - +
93A GLY 2.8 37.2 + - - -
94A VAL 3.6 6.5 - - - -
95A CYS* 3.9 9.7 - - - -
182A GLN* 3.7 22.8 + - + +
183A GLU* 2.8 26.1 + - - +
184A ALA 3.2 23.0 + - - -
185A CYS* 3.5 19.1 - - - +
186A PRO* 5.4 1.4 - - - +
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Residues in contact with THR 90 (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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65A PRO* 3.5 15.4 + - + +
67A ASP* 4.0 1.8 - - - -
88A ILE* 3.6 5.7 + - - +
89A ARG* 1.3 76.8 - - - +
91A LYS* 1.3 55.1 + - - +
92A SER* 2.7 36.6 - - - +
93A GLY* 2.7 28.6 + - - +
94A VAL* 3.0 27.4 + - + +
96A VAL* 4.0 17.0 - - - +
182A GLN* 3.4 8.7 + - - -
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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