Contacts of the strand formed by residues 27 - 33 (chain D) in PDB entry 1R6Q
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 MET 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B PHE* 6.4 0.2 - - - -
65B THR* 5.3 9.6 - - + -
25D PRO 5.6 1.8 - - - +
26D SER* 1.3 81.8 + - - +
28D TYR* 1.3 63.8 + - - +
75D VAL* 4.0 16.2 - - + +
76D PHE* 3.4 31.9 - - - +
77D THR* 3.8 20.6 - - + +
106D ALA* 2.8 36.5 + - + +
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Residues in contact with TYR 28 (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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117B GLU* 2.5 34.4 + - - -
146B GOL 3.8 17.8 + - - -
26D SER* 3.4 24.5 - - - -
27D MET* 1.3 74.1 - - - +
29D LYS* 1.3 65.3 + - - +
30D VAL* 3.8 0.5 + - - +
75D VAL* 3.4 4.3 - - - -
76D PHE* 2.7 34.7 + - - +
78D ALA* 3.6 21.5 - - + -
81D ALA* 3.8 22.8 - - + +
103D LEU* 4.1 16.4 - - + -
104D GLU* 3.3 24.7 - - - +
105D LYS* 3.4 32.7 + - + +
106D ALA* 3.9 0.7 - - - +
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Residues in contact with LYS 29 (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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28D TYR* 1.3 72.8 - - - +
30D VAL* 1.3 59.7 + - - +
31D ILE* 3.9 11.2 + - + +
72D ILE* 3.8 35.0 - - + +
74D GLY 3.3 9.0 - - - +
75D VAL* 4.3 12.3 - - + +
103D LEU* 3.1 8.1 - - - +
104D GLU* 2.7 52.0 + - - +
105D LYS 4.3 5.5 + - - +
106D ALA* 4.0 33.8 + - + +
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Residues in contact with VAL 30 (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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29D LYS* 1.3 72.8 - - - +
31D ILE* 1.3 57.8 + - - +
51D PHE* 3.7 26.2 - - + -
72D ILE* 3.6 2.1 - - - -
73D CYS* 2.6 34.8 + - + +
74D GLY 2.8 12.6 + - - +
76D PHE* 3.6 26.7 - - + -
81D ALA* 3.7 31.2 - - + +
84D LYS* 4.8 2.2 - - + -
85D VAL* 4.0 9.6 - - + +
101D CYS* 3.6 27.4 - - - -
102D THR 3.5 5.6 - - - +
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Residues in contact with ILE 31 (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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29D LYS* 4.4 11.4 - - + +
30D VAL* 1.3 80.7 - - - +
32D LEU* 1.3 74.3 + - - +
33D VAL* 4.1 3.3 + - + -
70D LYS* 3.8 31.2 - - + +
71D ALA 3.4 11.2 - - - +
72D ILE* 4.2 17.7 - - + -
73D CYS* 4.5 1.3 - - - -
100D LEU 4.0 0.2 - - - +
101D CYS* 3.2 10.8 - - - -
102D THR* 2.7 53.8 + - - +
104D GLU* 3.8 39.3 - - + +
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Residues in contact with LEU 32 (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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31D ILE* 1.3 75.0 - - - +
33D VAL* 1.3 61.0 + - - +
43D VAL* 4.2 15.5 - - + -
46D VAL* 4.2 13.0 - - + -
47D LEU* 3.7 36.6 - - + -
51D PHE* 5.2 0.7 - - + -
65D VAL* 3.9 17.3 - - + +
70D LYS* 3.1 5.4 - - - +
71D ALA 3.0 29.9 + - - +
73D CYS* 3.7 12.7 - - - -
88D VAL* 4.2 12.6 - - + -
99D LEU* 4.1 21.5 - - + -
100D LEU 3.7 12.3 - - - +
101D CYS* 4.1 22.0 - - + -
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Residues in contact with VAL 33 (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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31D ILE* 4.4 6.5 - - + -
32D LEU* 1.3 76.7 - - - +
34D ASN* 1.3 76.6 + - - +
35D ASP* 3.9 1.6 + - - +
65D VAL* 3.8 3.5 - - - +
69D GLY 3.8 10.3 - - - +
70D LYS* 4.3 5.6 - - + -
99D LEU* 3.7 21.1 - - - +
100D LEU* 2.9 37.8 + - + +
102D THR* 4.1 30.3 - - + +
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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