Contacts of the strand formed by residues 78 - 85 (chain A) in PDB entry 1HKC
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 GLY 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LYS* 1.3 85.6 - - - +
79A ASP* 1.3 62.4 + - - +
80A PHE* 3.8 15.6 - - - -
96A GLN* 3.7 4.5 - - - +
97A VAL 2.5 34.9 + - - +
98A ASN* 5.0 0.9 - - - +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY* 1.3 75.0 - - - +
80A PHE* 1.3 65.8 + - - +
94A ARG* 2.6 44.5 + - - -
95A VAL 3.5 10.1 - - - +
96A GLN* 3.5 24.6 + - - +
146A LYS* 4.0 6.8 + - - -
148A LEU* 3.3 23.1 - - + +
149A PRO* 3.3 19.8 - - - +
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS 4.3 2.2 - - - -
78A GLY* 3.8 31.0 - - - -
79A ASP* 1.3 77.6 + - - +
81A ILE* 1.3 71.3 + - - +
94A ARG* 3.5 5.4 - - - +
95A VAL* 3.0 39.5 + - - +
97A VAL* 4.3 14.1 - - + -
148A LEU* 4.3 3.6 - - - -
149A PRO* 3.1 33.9 - - + +
454A ALA* 3.7 26.0 - - + -
457A THR* 3.4 22.2 - - + -
458A ALA* 3.5 39.3 - - + -
461A TYR* 5.5 3.8 - + + -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PHE* 1.3 80.5 - - - +
82A ALA* 1.3 72.3 + - - +
83A LEU* 4.2 8.1 - - + -
92A ILE* 3.9 20.0 - - + -
93A LEU 3.2 12.1 - - - +
94A ARG* 3.6 19.7 - - + -
95A VAL* 6.0 0.2 - - - -
134A LEU* 4.5 7.2 - - + -
137A PHE* 4.1 9.6 - - + -
138A MET* 5.0 10.5 - - + -
143A ILE* 3.7 14.4 - - + -
148A LEU* 3.5 37.2 - - + -
149A PRO 3.0 5.5 + - - +
150A VAL* 4.0 19.1 - - + -
151A GLY* 3.0 22.3 + - - -
454A ALA* 5.6 2.6 - - - -
457A THR* 5.0 0.5 + - - -
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 1.3 79.5 - - - +
83A LEU* 1.3 65.9 + - - +
92A ILE* 3.4 3.8 - - - +
93A LEU* 2.6 59.3 + - + +
95A VAL* 4.8 4.5 - - + -
151A GLY 3.3 7.4 - - - +
449A SER 5.3 0.2 - - - +
450A GLY* 3.9 18.2 - - - +
453A ALA* 4.5 13.2 - - + -
454A ALA* 5.2 3.1 - - + +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 4.2 10.1 - - + -
82A ALA* 1.3 83.9 - - - +
84A ASP* 1.3 61.3 + - - +
85A LEU 4.1 0.4 - - - -
90A PHE* 4.7 5.2 - - + -
91A ARG 4.0 3.8 - - - -
92A ILE* 3.9 25.8 - - + -
93A LEU* 4.9 0.4 - - - -
130A VAL* 4.4 17.7 - - + -
134A LEU* 4.3 19.5 - - + -
150A VAL* 4.2 19.7 - - + -
151A GLY 2.9 11.4 + - - +
152A PHE* 3.8 21.0 - - + -
153A THR* 2.8 29.8 + - - -
189A LEU* 4.2 24.7 - - + -
453A ALA* 5.3 0.2 - - - +
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 1.3 75.7 - - - +
85A LEU* 1.3 67.6 + - - +
87A GLY* 4.9 4.9 + - - -
89A SER 3.7 3.4 - - - +
90A PHE* 3.3 18.7 - - - -
91A ARG* 3.1 54.7 + - + +
93A LEU* 4.6 6.5 - - + -
153A THR* 3.5 21.2 - - - +
155A SER* 4.7 4.2 + - - -
209A ASP* 5.5 1.8 - - - +
447A SER* 5.1 3.8 + - - +
449A SER* 3.9 20.6 + - - +
450A GLY* 5.3 0.7 + - - -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU 4.1 0.2 - - - -
84A ASP* 1.3 76.1 + - - +
86A GLY* 1.3 60.3 + - - +
87A GLY 3.7 1.6 - - - -
90A PHE* 3.9 33.7 - - + +
114A THR* 5.1 5.2 - - + +
126A LEU* 4.6 13.5 - - + -
127A PHE* 5.3 3.1 - - + -
129A HIS* 6.5 0.4 - - + -
130A VAL* 4.0 24.5 - - + -
152A PHE* 4.0 17.7 - - + -
153A THR 3.0 10.2 + - - +
154A PHE* 3.6 29.4 - - + -
155A SER* 3.4 22.7 + - - -
175A PHE* 3.7 32.3 - - + -
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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