Contacts of the helix formed by residues 89 - 103 (chain A) in PDB entry 2HKU
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 THR 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ALA 3.3 5.5 - - - +
88A GLU* 1.3 78.9 + - + +
90A VAL* 1.3 52.5 + - - +
91A GLY* 3.1 4.3 + - - -
92A ASP* 3.0 22.4 + - + +
93A TYR* 2.7 31.3 + - - +
206A ARG 2.7 21.7 + - - -
207A ASN* 3.8 13.4 - - - +
208A THR 3.2 13.2 - - - -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 4.9 5.2 - - - +
89A THR* 1.3 69.8 + - - +
91A GLY* 1.3 66.8 + - - +
92A ASP 2.9 1.1 - - - -
93A TYR* 2.9 16.1 + - + +
94A THR* 2.9 20.0 + - - +
147A THR* 4.3 16.8 - - + -
148A LEU* 4.2 22.0 - - + -
150A ARG* 6.3 0.2 - - - +
151A THR* 3.6 38.8 - - + +
201A ILE* 4.9 2.9 - - + -
205A VAL* 3.4 27.8 - - + +
206A ARG* 4.3 1.1 - - - -
208A THR 2.6 17.4 + - - +
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 3.9 0.2 - - - -
90A VAL* 1.3 73.4 - - - +
92A ASP* 1.3 57.1 + - - +
94A THR* 3.6 6.0 + - - -
95A GLU* 3.1 39.1 + - - +
196A PHE* 4.0 3.6 - - - -
201A ILE* 5.6 1.6 - - - -
206A ARG* 2.8 45.7 + - - -
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 4.5 1.3 - - - +
88A GLU 4.4 2.9 - - - -
89A THR* 3.0 36.6 + - - +
90A VAL 2.9 0.4 - - - -
91A GLY* 1.3 77.3 - - - +
93A TYR* 1.3 57.7 + - - +
95A GLU* 3.7 17.5 + - - +
96A LYS* 3.1 53.3 + - - +
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Residues in contact with TYR 93 (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 GLU* 4.8 4.2 + - - -
84A ALA* 2.9 51.9 - - + +
85A ALA* 4.0 9.6 - - + -
87A ALA 4.2 4.9 - - - +
89A THR 2.7 16.3 + - - +
90A VAL* 3.3 13.0 - - + +
92A ASP* 1.3 74.2 - - - +
94A THR* 1.3 62.3 + - - +
96A LYS* 3.4 1.7 + - - +
97A LEU* 2.7 41.3 + - + +
143A ALA* 3.2 24.8 - - - +
144A LEU* 3.5 20.8 + - + -
147A THR* 3.1 43.6 + - + -
148A LEU* 6.0 0.4 - - + -
150A ARG* 6.3 0.2 - - - -
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Residues in contact with THR 94 (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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90A VAL 2.9 14.6 + - - -
91A GLY 3.8 4.3 - - - -
93A TYR* 1.3 82.6 - - - +
95A GLU* 1.3 55.5 + - - +
97A LEU* 3.9 2.9 - - - +
98A VAL* 3.0 45.2 + - + +
144A LEU* 3.9 17.8 - - + +
148A LEU* 4.1 5.5 - - - +
195A ILE* 5.1 0.2 - - + -
196A PHE* 3.8 23.1 - - + -
199A LEU* 3.8 26.7 - - + -
201A ILE* 3.9 13.8 - - + +
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Residues in contact with GLU 95 (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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91A GLY* 3.1 27.9 + - - +
92A ASP* 3.9 17.6 + - - +
93A TYR 3.3 0.2 - - - -
94A THR* 1.3 72.2 - - - +
96A LYS* 1.3 62.5 + - + +
98A VAL* 4.9 0.2 - - - -
99A GLY* 2.7 29.3 + - - +
192A VAL* 5.4 5.3 - - + +
196A PHE* 3.6 25.9 - - + -
206A ARG* 6.1 0.7 - - - -
304A EDO 6.1 1.3 - - - -
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Residues in contact with LYS 96 (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 ALA 4.5 1.5 - - - +
83A ASP* 3.6 23.6 + - + +
84A ALA* 3.9 12.1 - - - +
86A THR* 4.3 19.3 + - - -
87A ALA* 4.3 14.4 - - - +
92A ASP* 3.1 39.2 + - - +
93A TYR 3.4 4.0 - - - +
95A GLU* 1.3 80.4 - - + +
97A LEU* 1.3 68.7 + - - +
99A GLY* 5.1 0.2 - - - -
100A SER* 3.0 22.7 + - - -
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Residues in contact with LEU 97 (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 ALA* 3.5 28.8 - - + +
81A GLU* 4.2 7.6 - - + +
84A ALA* 3.7 6.9 - - + +
93A TYR* 2.7 51.2 + - + +
94A THR* 3.4 4.7 + - - +
96A LYS* 1.3 76.7 - - - +
98A VAL* 1.3 61.2 + - + +
100A SER* 3.1 9.9 + - - -
101A LEU* 3.2 22.4 + - + +
144A LEU* 4.1 7.9 - - + -
166A PHE* 3.6 30.1 - - + -
302A EDO 3.7 29.2 - - - +
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Residues in contact with VAL 98 (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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94A THR* 3.0 26.7 + - + +
95A GLU* 4.4 1.3 - - - +
97A LEU* 1.3 73.7 - - + +
99A GLY* 1.3 67.2 + - - +
100A SER 3.2 0.3 + - - -
101A LEU* 3.3 5.4 + - - +
102A LEU* 2.9 49.9 + - + +
144A LEU* 5.9 0.2 - - + -
166A PHE* 3.8 15.5 - - + -
170A ILE* 4.6 2.7 - - + -
192A VAL* 3.9 18.6 - - + +
195A ILE* 3.7 39.9 - - + -
196A PHE* 4.9 2.0 - - + -
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Residues in contact with GLY 99 (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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95A GLU 2.7 23.5 + - - -
96A LYS* 3.9 0.4 - - - -
98A VAL* 1.3 75.0 - - - +
100A SER* 1.3 55.3 + - - -
102A LEU* 4.7 0.9 - - - -
103A GLY* 3.0 25.9 + - - -
104A PRO* 3.5 4.4 - - - +
188A LEU* 4.8 5.6 - - - +
192A VAL* 4.3 14.8 - - - +
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Residues in contact with SER 100 (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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76A ALA 4.8 1.2 + - - -
79A ARG* 4.1 12.9 + - - +
80A ALA* 3.6 27.5 + - - +
83A ASP* 4.8 8.2 + - - -
96A LYS 3.0 15.2 + - - -
97A LEU 3.1 9.2 + - - -
99A GLY* 1.3 73.0 - - - +
101A LEU* 1.3 59.6 + - - +
104A PRO* 3.3 19.9 - - - +
105A GLY* 2.6 34.9 + - - -
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Residues in contact with LEU 101 (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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76A ALA* 3.5 39.7 - - + +
77A GLY* 3.8 7.0 - - - +
80A ALA* 3.6 12.3 - - + -
97A LEU* 3.2 14.0 + - + +
98A VAL 4.0 4.3 - - - +
100A SER* 1.3 80.6 - - - +
102A LEU* 1.3 60.1 + - - +
105A GLY* 3.4 5.1 - - - +
106A ALA* 3.2 24.9 + - - +
109A VAL* 4.2 11.4 - - + +
166A PHE* 3.8 35.4 - - + -
167A TRP* 4.0 22.7 - - + -
170A ILE* 4.2 19.3 - - + -
174A VAL* 4.3 1.6 - - - +
302A EDO 4.7 0.9 - - - -
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Residues in contact with LEU 102 (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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98A VAL* 2.9 40.3 + - + +
101A LEU* 1.3 75.2 - - - +
103A GLY* 1.3 59.4 + - - +
106A ALA* 3.3 7.1 - - - +
170A ILE* 3.9 23.1 - - + +
173A LEU* 4.1 17.3 - - + -
174A VAL* 3.8 24.0 - - + +
177A LYS* 2.7 35.8 + - - -
188A LEU* 3.7 18.0 - - + +
191A ALA* 3.7 32.8 - - + +
192A VAL* 3.7 4.9 - - + +
195A ILE* 4.5 3.1 - - + -
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Residues in contact with GLY 103 (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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99A GLY 3.0 13.0 + - - -
101A LEU 3.3 0.6 - - - -
102A LEU* 1.3 76.9 - - - +
104A PRO* 1.4 73.3 - - - +
105A GLY 3.2 0.2 - - - -
106A ALA* 3.2 16.6 + - - +
107A PRO* 3.9 4.0 - - - +
188A LEU* 4.1 13.2 - - - +
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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