Contacts of the strand formed by residues 65 - 72 (chain D) in PDB entry 1QZH
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 TRP 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D SER* 4.0 7.9 - - - -
56D ARG* 3.4 17.5 - - - -
57D GLN* 3.4 61.9 - - + +
64D ASP* 1.3 75.5 - - - +
66D VAL* 1.3 59.3 + - - +
87D LEU 3.6 0.3 - - - +
88D PHE* 3.2 6.2 - - - -
89D SER* 2.9 35.6 + - - +
92D GLY* 3.7 31.5 - - - +
93D ASN* 4.1 29.9 - - + +
95D LEU* 3.9 13.7 - - + -
148F MET* 4.5 25.8 - - + -
149F PRO* 6.3 0.9 - - + -
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Residues in contact with VAL 66 (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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55D SER* 3.6 0.5 - - - -
56D ARG* 2.9 69.4 + - + +
58D SER* 3.6 19.3 - - - +
65D TRP* 1.3 76.2 - - - +
67D THR* 1.3 72.3 + - - +
68D THR* 4.3 4.3 - - - +
86D HIS* 4.4 8.3 - - + +
87D LEU 3.2 8.3 - - - +
88D PHE* 3.7 29.4 - - + -
95D LEU* 3.9 2.9 - - - +
5J A 4.4 9.2 - - - +
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Residues in contact with THR 67 (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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52D PHE* 5.7 1.0 - - - +
53D THR 2.9 21.2 + - - -
54D PRO* 4.4 0.9 - - - +
55D SER* 3.8 20.3 + - - -
66D VAL* 1.3 76.5 - - - +
68D THR* 1.3 61.6 + - - +
69D VAL* 4.9 6.5 - - + +
85D ILE 3.9 0.5 - - - +
86D HIS* 3.9 0.5 - - - -
87D LEU* 2.9 62.4 + - + +
95D LEU* 3.7 19.7 - - + -
96D PRO* 4.1 11.2 + - + +
98D ILE* 5.3 3.2 - - + +
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Residues in contact with THR 68 (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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52D PHE* 3.1 4.2 - - - +
53D THR* 2.7 41.6 + - - +
56D ARG* 2.9 26.4 + - - +
66D VAL* 4.3 0.5 - - - +
67D THR* 1.3 74.7 + - - +
69D VAL* 1.3 68.9 + - - +
70D TYR* 3.9 25.4 - - + +
84D GLN* 4.1 8.7 - - + -
85D ILE 3.4 7.6 - - - +
86D HIS* 2.6 38.7 + - + -
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Residues in contact with VAL 69 (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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49D VAL* 4.9 5.4 - - + -
51D ASP 3.5 5.6 - - - +
52D PHE* 4.0 4.7 - - + -
67D THR* 4.9 3.6 - - - +
68D THR* 1.3 82.4 - - - +
70D TYR* 1.3 66.3 + - - +
71D LEU* 4.9 3.8 - - + -
83D LEU 3.4 1.2 - - - +
84D GLN* 3.7 1.4 - - - -
85D ILE* 2.9 55.4 + - + +
87D LEU* 4.3 23.3 - - + -
98D ILE* 3.4 33.2 - - + -
105D LEU* 4.4 15.9 - - + -
107D LEU* 4.8 0.7 - - + -
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Residues in contact with TYR 70 (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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48D ILE 3.5 0.5 - - - +
49D VAL* 3.8 1.9 - - - -
50D LYS* 2.8 30.3 + - - +
51D ASP* 2.9 45.1 + - + +
52D PHE* 4.6 0.7 - - - -
53D THR* 5.0 7.2 - - - -
68D THR* 3.9 17.1 - - + +
69D VAL* 1.3 74.4 - - - +
71D LEU* 1.3 61.7 + - - +
81D ILE* 3.6 36.8 - - + +
82D GLY 4.5 4.5 - - - -
83D LEU 3.2 6.5 - - - +
84D GLN* 3.0 52.1 + - + -
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Residues in contact with LEU 71 (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 ILE* 3.7 23.6 - - + +
45D LEU* 3.7 30.5 - - + -
46D PHE 4.5 0.4 - - - +
47D GLY* 3.8 28.3 - - - +
48D ILE 3.4 17.7 - - - +
49D VAL* 4.3 4.5 - - + +
69D VAL* 4.0 5.6 - - + -
70D TYR* 1.3 73.4 - - - +
72D TRP* 1.3 59.8 + - - +
82D GLY* 3.1 6.0 - - - -
83D LEU* 2.9 38.2 + - + +
85D ILE* 3.8 21.1 - - + -
105D LEU* 4.4 20.9 - - + +
107D LEU* 4.4 8.1 - - + -
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Residues in contact with TRP 72 (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 ILE* 4.1 2.7 - - - -
47D GLY* 3.4 1.4 - - - -
48D ILE* 2.7 53.4 + - + +
50D LYS* 4.0 24.9 - - + -
71D LEU* 1.3 76.0 - - - +
73D ASP* 1.3 85.0 + - - +
74D PRO* 3.8 21.5 - - + -
76D CYS* 3.6 23.0 + - + +
77D ASP 3.5 21.1 + - - -
78D THR* 3.8 10.2 - - - +
80D SER 4.3 11.9 - - - -
82D GLY* 4.8 2.9 - - - -
165D LEU 4.3 2.5 - - - -
168D ILE* 4.3 1.6 - - + -
169D TRP* 3.5 53.4 - + + -
172D GLN* 3.8 28.9 - - + -
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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