Contacts of the strand formed by residues 73 - 78 (chain D) in PDB entry 1ZQ1
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 VAL 73 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLN* 3.3 44.2 - - + +
48D ARG 3.7 9.6 - - - +
49D ARG* 4.1 13.9 - - - -
71D GLY 5.2 1.6 - - - +
72D ARG* 1.3 75.6 - - - +
74D TYR* 1.3 66.8 + - - +
75D VAL* 3.8 2.0 + - + -
174D LYS 3.1 17.5 + - - +
175D GLU* 3.2 19.9 - - + +
176D VAL 3.1 21.0 + - - -
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Residues in contact with TYR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN* 3.5 2.6 - - - -
48D ARG 2.6 46.7 + - - +
49D ARG* 5.1 0.4 - - - -
50D LEU* 3.5 36.2 - - + +
67D GLU* 3.3 26.2 + - - +
72D ARG* 4.2 23.8 - - + +
73D VAL* 1.3 75.9 - - - +
75D VAL* 1.3 62.5 + - - +
76D TYR* 3.4 29.1 - + + +
127D ILE 3.3 13.3 + - - -
128D ASP 3.4 17.0 + - - -
129D GLY* 3.4 24.2 - - - +
176D VAL* 3.6 22.9 - - + +
178D TYR* 4.7 1.8 - + + -
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 3.2 30.1 - - + +
46D PHE 3.6 7.9 - - - +
47D GLN* 4.8 12.8 - - + -
73D VAL* 4.4 2.5 - - + +
74D TYR* 1.3 75.5 - - - +
76D TYR* 1.3 62.4 + - - +
77D GLU* 5.4 0.4 - - + -
175D GLU* 3.8 35.4 - - + +
176D VAL 2.9 9.8 + - - +
177D ILE* 3.3 20.0 - - + +
178D TYR* 2.8 26.7 + - - +
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Residues in contact with TYR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D PHE 4.0 0.2 - - - +
45D THR* 2.7 24.2 + - - -
46D PHE* 2.9 62.1 + + + -
48D ARG* 3.7 14.2 - - + +
50D LEU* 5.2 2.6 - - - +
74D TYR* 3.4 41.4 - - + +
75D VAL* 1.3 73.8 - - - +
77D GLU* 1.3 58.5 - - - +
129D GLY* 2.5 31.9 + - - -
130D SER 5.2 2.0 - - - -
131D ASN 4.6 0.2 - - - -
132D VAL* 3.3 36.8 - - + -
166D ALA* 5.5 1.6 - - + -
178D TYR* 3.3 24.9 - + + -
180D LEU* 3.7 16.2 - - + -
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Residues in contact with GLU 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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42D VAL* 3.5 37.9 - - + +
44D PHE 3.7 4.9 - - - -
45D THR* 4.0 9.2 - - - +
75D VAL* 5.4 0.2 - - + -
76D TYR* 1.3 75.2 - - - +
78D GLY* 1.3 57.5 + - - +
169D ILE* 3.3 19.2 - - - +
177D ILE* 3.8 23.6 - - + +
178D TYR 2.8 8.3 + - - +
179D ARG* 3.0 34.9 + - - +
180D LEU* 3.0 31.7 + - - +
181D ASP 4.8 0.2 + - - -
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Residues in contact with GLY 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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41D LYS 4.7 2.2 - - - -
42D VAL* 4.7 1.5 - - - +
43D GLU 3.0 18.7 + - - -
44D PHE* 3.0 31.3 + - - +
76D TYR 4.2 0.4 + - - -
77D GLU* 1.3 76.9 - - - +
79D ASN* 1.3 61.5 + - - -
83D THR* 3.1 20.4 - - - -
179D ARG* 5.9 0.7 - - - -
180D LEU* 4.3 0.9 - - - +
181D ASP 5.8 1.1 - - - -
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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
------------------------------------------------------------
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