Contacts of the helix formed by residues 87 - 95 (chain D) in PDB entry 1Q57
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 SER 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D ALA* 3.7 3.1 - - - -
86D ILE* 1.3 79.0 - - - +
88D LYS* 1.3 66.0 + - - +
89D GLU* 4.2 8.2 - - - +
90D THR* 3.1 22.3 + - - -
91D CYS* 3.3 13.0 + - - -
167D GLU* 2.7 34.2 + - - -
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Residues in contact with LYS 88 (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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78D TYR* 2.9 33.5 - - + +
79D SER* 4.1 7.6 - - - -
80D ALA* 3.1 28.9 - - + +
87D SER* 1.3 74.3 - - - +
89D GLU* 1.3 66.5 + - - +
90D THR 3.2 0.3 + - - -
91D CYS* 3.4 3.8 + - - +
92D GLN* 3.2 23.2 + - + +
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Residues in contact with GLU 89 (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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87D SER* 4.7 6.3 - - - +
88D LYS* 1.3 82.9 - - - +
90D THR* 1.3 56.8 + - - +
92D GLN* 3.4 13.4 - - + +
93D LYS* 3.0 59.3 + - - +
170D ASP* 5.0 7.4 - - - +
171D CYS* 5.2 3.6 - - - -
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Residues in contact with THR 90 (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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86D ILE* 3.3 22.9 - - + -
87D SER* 3.1 26.7 + - - -
88D LYS 3.1 0.8 - - - -
89D GLU* 1.3 74.1 + - - +
91D CYS* 1.3 67.7 + - - +
92D GLN 3.0 1.3 - - - -
93D LYS* 2.8 17.2 + - - +
94D ALA* 3.4 9.2 + - - +
163D LEU* 3.5 27.4 - - + +
166D MET* 4.4 10.0 - - + +
167D GLU* 3.2 14.5 + - + +
171D CYS* 3.6 20.7 - - - -
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Residues in contact with CYS 91 (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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78D TYR* 4.2 2.2 - - + -
79D SER 3.8 16.4 - - - +
81D LEU* 3.3 42.2 - - - -
86D ILE* 3.8 5.8 - - - -
87D SER 3.3 6.7 + - - -
88D LYS 3.8 7.2 - - - +
90D THR* 1.3 79.2 - - - +
92D GLN* 1.3 57.4 + - - +
94D ALA 4.9 0.4 - - - +
95D GLY* 3.0 10.6 + - - -
96D TYR* 2.8 49.5 + - - +
163D LEU* 3.6 17.7 - - - -
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Residues in contact with GLN 92 (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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78D TYR* 3.2 54.6 + - + +
88D LYS* 3.2 14.5 + - + +
89D GLU* 3.4 17.5 - - + +
90D THR 2.9 1.0 + - - -
91D CYS* 1.3 80.5 - - - +
93D LYS* 1.3 61.7 + - + +
95D GLY* 3.9 4.2 + - - -
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Residues in contact with LYS 93 (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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89D GLU* 3.0 52.4 + - - +
90D THR 2.8 11.4 + - - +
92D GLN* 1.3 74.8 - - + +
94D ALA* 1.3 61.8 + - - +
95D GLY* 3.3 1.7 + - - -
145D HIS* 4.7 2.6 - - - -
146D LEU* 3.6 23.2 - - + +
166D MET* 4.6 11.2 - - + -
170D ASP* 5.1 4.8 + - - -
171D CYS* 4.2 23.5 - - + +
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Residues in contact with ALA 94 (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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90D THR 3.4 7.6 + - - +
91D CYS 4.6 1.1 - - - +
93D LYS* 1.3 78.9 - - - +
95D GLY* 1.3 58.5 + - - +
96D TYR 4.8 0.2 - - - +
110D ASP 4.2 5.2 - - - +
142D PHE* 3.2 26.2 - - + -
143D GLY* 5.2 0.7 - - - -
145D HIS* 4.3 11.8 + - - -
146D LEU* 4.0 9.1 - - - +
162D MET* 3.4 31.7 - - + +
163D LEU* 3.8 14.1 - - + -
166D MET* 4.1 8.9 - - - -
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Residues in contact with GLY 95 (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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78D TYR* 4.4 15.3 - - - -
91D CYS 3.0 5.4 + - - -
92D GLN 3.9 3.3 + - - -
93D LYS 3.3 3.4 - - - -
94D ALA* 1.3 82.3 - - - +
96D TYR* 1.3 61.4 + - - +
97D TRP* 3.8 3.9 + - - -
108D VAL 3.6 2.1 - - - +
109D ALA* 3.8 1.2 - - - -
110D ASP* 3.0 40.7 + - - +
112D ARG* 5.8 3.8 - - - -
142D PHE* 3.9 2.5 - - - -
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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