Contacts of the helix formed by residues 94 - 104 (chain A) in PDB entry 1K30
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 ASP 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ARG* 2.9 63.0 + - - +
91A GLU* 4.9 4.3 - - - +
92A PRO 3.9 2.6 + - - -
93A PHE* 1.3 74.0 - - - +
95A TYR* 1.3 61.1 + - - +
96A TYR 3.2 3.1 + - - -
97A ILE* 3.0 36.9 + - + +
98A PHE* 3.0 21.1 + - - +
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Residues in contact with TYR 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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71A ARG* 2.9 46.8 + - + +
74A LEU* 3.8 9.9 - - - +
89A ILE* 3.1 22.8 + - + +
93A PHE* 3.1 44.9 + + + -
94A ASP* 1.3 71.1 - - - +
96A TYR* 1.3 61.3 + - - +
98A PHE* 3.6 3.9 - + - +
99A GLY* 3.0 19.8 + - - -
179A PRO* 3.2 40.8 - - + +
180A PHE 4.8 1.4 - - - +
182A ILE* 3.6 30.2 - - + +
183A GLY* 3.4 24.1 - - - +
184A ARG* 5.1 0.3 + - - -
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 4.9 1.6 - - + -
89A ILE 3.8 1.4 + - - -
90A ARG* 3.4 44.6 - - - +
94A ASP* 3.2 1.2 + - - -
95A TYR* 1.3 73.9 - - - +
97A ILE* 1.3 72.2 + - + +
99A GLY 3.1 3.1 + - - -
100A GLN* 3.0 39.4 + - + +
149A SER* 3.5 12.8 - - - -
153A GLU* 5.7 1.0 - - - +
160A ALA* 3.4 34.6 + - - +
161A GLU* 3.9 26.2 - - + +
183A GLY* 3.3 27.0 - - - +
184A ARG* 3.4 39.0 + - - +
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Residues in contact with ILE 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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90A ARG* 3.8 13.9 - - - +
94A ASP* 3.0 34.6 + - + +
96A TYR* 1.3 83.1 - - + +
98A PHE* 1.3 63.2 + - - +
100A GLN* 3.3 8.8 + - + +
101A ASN* 2.9 44.6 + - - +
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Residues in contact with PHE 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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64A ASN* 3.8 19.7 - - - -
67A VAL* 3.7 23.1 - - + -
68A ALA* 3.5 40.4 - - + -
71A ARG* 4.9 1.1 - - + -
93A PHE* 3.8 24.9 - + + -
94A ASP 3.0 18.0 + - - +
95A TYR* 3.6 8.1 - + - +
96A TYR 3.2 0.2 - - - -
97A ILE* 1.3 77.3 - - - +
99A GLY* 1.3 60.9 + - - +
101A ASN* 3.8 6.1 - - + +
102A TYR* 2.8 47.6 + + + +
179A PRO* 4.3 24.7 - - + -
180A PHE* 5.5 1.1 - - - -
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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 TYR 3.0 14.5 + - - -
96A TYR 3.1 2.8 + - - -
98A PHE* 1.3 78.7 - - - +
100A GLN* 1.3 64.3 + - - +
102A TYR* 3.3 5.7 + - - +
103A ILE* 3.0 30.1 + - - +
146A ALA* 4.4 0.2 - - - +
180A PHE* 3.7 27.1 - - - -
184A ARG* 3.6 8.7 - - - -
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Residues in contact with GLN 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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96A TYR* 3.0 42.6 + - + +
97A ILE* 3.5 11.2 - - + +
99A GLY* 1.3 76.8 - - - +
101A ASN* 1.3 58.9 + - - +
103A ILE 3.3 0.3 + - - -
104A ARG* 2.9 34.0 + - - +
146A ALA* 3.5 8.2 - - - -
149A SER* 3.3 28.7 + - - -
150A LEU* 3.4 38.6 - - + +
153A GLU* 4.4 6.1 + - - +
184A ARG* 2.8 31.4 + - - +
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Residues in contact with ASN 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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64A ASN* 3.1 24.8 + - - +
97A ILE* 2.9 40.6 + - - +
98A PHE* 3.9 6.8 - - + +
100A GLN* 1.3 70.1 - - - +
102A TYR* 1.3 65.4 + - - +
104A ARG* 4.0 22.8 + - - +
105A PRO* 3.2 14.7 - - - +
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Residues in contact with TYR 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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41A LEU* 3.5 35.5 - - + +
45A TYR* 2.6 70.0 + + - -
64A ASN* 3.7 15.0 - - + +
65A MET* 4.1 12.9 - - - -
68A ALA* 4.1 12.6 - - + -
98A PHE* 2.8 38.2 + + + +
99A GLY* 3.6 8.3 - - - +
100A GLN 3.3 0.2 - - - -
101A ASN* 1.3 78.4 - - - +
103A ILE* 1.3 78.9 + - + +
105A PRO* 3.7 1.7 - - - +
106A LEU* 4.4 0.9 - - - +
180A PHE* 5.4 4.7 - + - -
282A MET* 4.7 9.6 - - + +
298A ILE* 4.8 1.0 - - - +
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Residues in contact with ILE 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 16.1 + - - +
102A TYR* 1.3 93.5 - - + +
104A ARG* 1.3 67.4 + - - +
105A PRO 3.4 0.9 - - - -
106A LEU* 2.9 28.6 + - + +
107A ILE* 3.8 5.7 + - + +
143A ALA* 3.7 22.2 - - + -
146A ALA* 3.8 24.9 - - + -
147A ILE* 4.2 19.7 - - + -
150A LEU* 3.9 14.4 - - + -
180A PHE* 4.1 9.9 - - + -
281A ILE* 5.2 2.2 - - + -
282A MET* 3.7 19.5 - - + -
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Residues in contact with ARG 104 (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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100A GLN* 2.9 20.4 + - - +
101A ASN* 4.0 21.9 + - - +
103A ILE* 1.3 75.0 - - - +
105A PRO* 1.3 69.4 - - + +
106A LEU 3.1 1.6 + - - -
107A ILE* 3.1 21.5 + - - +
109A PHE* 4.0 22.9 - - + -
150A LEU* 3.5 29.0 - - + +
153A GLU* 2.8 40.7 + - - -
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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