Contacts of the strand formed by residues 76 - 86 (chain D) in PDB entry 2QC8
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 ASP 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D ASN* 4.2 16.2 + - + +
62D PHE 3.5 8.3 - - - +
70D SER* 5.4 0.2 - - - -
74D ASN 4.3 1.0 - - - +
75D SER* 1.3 75.3 - - - +
77D MET* 1.3 63.3 + - - +
104D TYR* 4.4 5.0 + - - +
317E ALA* 3.5 15.4 - - - +
319E ARG* 3.0 17.3 + - - +
324E ARG* 3.0 31.5 + - - -
326E PRO* 3.8 2.1 - - - +
327E ARG* 2.9 63.2 + - + +
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Residues in contact with MET 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ASN* 2.8 27.7 - - - +
62D PHE* 2.9 32.8 + - + +
64D GLY* 3.7 11.4 - - - -
69D GLN* 3.5 41.7 - - + +
70D SER* 3.8 7.6 - - - +
75D SER 3.5 9.2 - - - +
76D ASP* 1.3 80.4 - - - +
78D TYR* 1.3 65.7 + - - +
101D VAL* 3.9 13.7 - - + -
102D PHE 3.5 16.6 - - - +
103D LYS* 3.8 28.9 - - + -
104D TYR 5.1 1.1 - - - +
109D ALA* 4.1 7.9 - - + -
110D GLU* 5.6 0.2 - - - +
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Residues in contact with TYR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 3.9 12.3 - - - -
60D TRP 3.5 9.0 - - - -
61D ASN* 4.2 2.9 - - + +
77D MET* 1.3 75.8 - - - +
79D LEU* 1.3 62.3 + - - +
80D VAL* 4.1 5.6 - - + -
100D GLU 3.6 0.3 - - - +
101D VAL* 3.4 11.4 - - - +
102D PHE* 3.1 45.8 + - + +
103D LYS 3.3 28.3 - - - -
104D TYR 4.0 5.0 + - - -
106D ARG* 3.4 50.1 + - + +
327E ARG* 3.5 36.2 - - + +
328E THR* 5.4 9.1 - - - -
331E GLN* 3.9 15.8 - - - +
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TYR* 4.2 19.2 - - + -
32D TRP* 3.6 51.8 - - + -
43D LYS* 4.6 0.7 - - - -
59D GLU* 3.4 8.0 - - - +
60D TRP* 2.7 47.7 + - + +
61D ASN 4.2 15.9 - - - +
62D PHE* 3.6 35.7 - - + -
78D TYR* 1.3 74.1 - - - +
80D VAL* 1.3 61.8 + - - +
81D PRO* 3.7 2.2 - - - +
99D CYS* 4.0 16.4 - - + -
100D GLU 3.7 0.9 - - - -
101D VAL* 4.2 4.0 - - + -
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 4.0 25.8 - - + +
78D TYR* 4.7 7.0 - - + -
79D LEU* 1.3 76.5 - - - +
81D PRO* 1.3 79.9 - - + +
82D ALA* 4.3 0.3 - - - +
99D CYS* 4.0 2.4 - - - +
100D GLU* 2.9 29.9 + - + +
102D PHE* 3.7 34.8 - - + -
106D ARG* 5.4 4.9 - - - +
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Residues in contact with PRO 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TYR* 4.1 11.9 - - + -
54D VAL* 3.8 22.3 - - + +
57D LEU* 3.9 20.2 - - + +
58D PRO 3.7 22.2 - - - +
59D GLU* 4.2 6.5 - - + +
79D LEU 3.7 8.7 - - - +
80D VAL* 1.3 98.2 - - + +
82D ALA* 1.3 58.7 + - - +
97D VAL* 3.6 14.8 - - + -
98D LEU 3.7 6.5 - - - +
99D CYS* 3.9 4.0 - - - -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D VAL* 3.7 15.6 - - - +
80D VAL 4.3 4.7 - - - +
81D PRO* 1.3 74.4 - - - +
83D ALA* 1.4 61.5 + - + +
98D LEU* 2.8 20.5 + - + +
99D CYS 4.6 0.4 - - - -
100D GLU* 4.4 7.0 - - + +
114D ARG* 3.5 50.1 + - - +
216D ASP* 4.7 0.8 - - - +
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D VAL* 3.8 4.9 - - - +
82D ALA* 1.4 80.2 - - - +
84D MET* 1.3 60.6 + - - +
85D PHE* 3.8 22.8 - - + -
96D LEU 3.8 0.5 - - - +
97D VAL* 3.4 3.4 - - - -
98D LEU* 2.8 39.7 + - + +
216D ASP* 3.7 28.9 - - + +
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PRO* 3.7 30.1 - - - +
52D LYS 4.1 2.9 - - - +
53D CYS* 3.5 33.0 - - - +
54D VAL* 3.9 20.8 - - + +
57D LEU* 3.9 24.0 - - + -
83D ALA* 1.3 74.0 - - - +
85D PHE* 1.3 79.6 + - - +
95D LYS* 4.1 19.7 - - + -
96D LEU 3.4 9.6 - - - +
97D VAL* 4.6 0.7 - - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ALA* 3.8 27.4 - - + -
84D MET* 1.3 82.5 - - - +
86D ARG* 1.3 66.2 + - - +
95D LYS* 3.3 10.1 - - - +
96D LEU* 2.8 39.6 + - + +
186D ALA* 3.5 20.6 - - + +
187D GLY* 3.7 24.5 - - - -
188D VAL* 4.1 9.6 - - + -
216D ASP 4.6 1.3 - - - -
217D HIS* 3.7 39.7 - + - -
220D VAL* 3.6 37.5 - - + -
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Residues in contact with ARG 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PRO* 5.1 6.1 + - - +
22C GLN 5.9 1.4 + - - -
85D PHE* 1.3 76.0 - - - +
87D ASP* 1.3 60.2 + - - +
88D PRO* 3.2 6.5 - - - +
92D ASP* 2.8 43.0 + - - +
94D ASN 3.9 5.4 - - - +
95D LYS* 4.6 11.2 - - + +
96D LEU* 4.1 2.3 - - - +
184D LEU 5.1 0.4 + - - -
185D TYR* 2.8 73.6 + - + +
186D ALA* 3.0 31.5 + - - +
187D GLY* 5.3 0.9 - - - +
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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