Contacts of the helix formed by residues 102 - 108 (chain A) in PDB entry 1K7E
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 TYR 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL 5.3 3.1 + - - -
54A PHE* 3.4 51.8 - + + +
56A ASP 4.4 1.6 - - - -
57A PRO* 3.3 14.9 - - + -
58A LEU* 3.5 23.8 - - + -
59A ALA* 3.0 27.7 + - + +
60A ASP* 2.4 33.9 + - - -
100A LEU* 4.1 15.3 - - + -
101A MET* 1.3 80.3 - - - +
103A ALA* 1.3 65.9 + - - +
104A ASN 3.1 1.0 + - - -
105A LEU* 3.2 15.8 + - + +
106A VAL 3.7 4.9 + - - -
128A VAL* 3.5 4.5 - - - +
129A ALA* 4.1 15.5 - - + -
130A ASP* 3.3 20.0 - - - +
401A IAG 4.5 0.7 + - - -
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Residues in contact with ALA 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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102A TYR* 1.3 70.7 - - - +
104A ASN* 1.3 68.2 + - - +
106A VAL* 2.9 13.2 + - - +
107A PHE* 3.0 13.5 + - - +
128A VAL* 3.6 9.6 - - - -
130A ASP* 2.6 25.6 + - - +
131A VAL* 3.8 20.2 - - + -
139A PHE* 4.6 3.7 - - + -
278B ILE* 3.5 33.0 - - + -
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Residues in contact with ASN 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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54A PHE* 4.1 17.9 - - + -
102A TYR* 3.1 2.6 + - - +
103A ALA* 1.3 82.6 - - - +
105A LEU* 1.3 58.1 + - - +
107A PHE* 4.5 4.6 - - - +
108A ASN* 2.8 35.3 + - - +
130A ASP* 4.6 0.4 + - - -
276B VAL 4.7 0.2 - - - +
277B GLY* 3.1 11.8 - - - -
278B ILE* 2.8 46.6 + - - +
288B GLN* 2.9 23.5 + - - +
292B GLY* 2.8 27.7 + - - -
294B ILE* 4.0 11.7 - - + +
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Residues in contact with LEU 105 (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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52A VAL* 3.7 15.9 - - + +
53A PRO 3.7 20.9 - - - +
54A PHE* 3.8 24.4 - - + -
78A PRO* 4.3 8.7 - - + -
101A MET* 3.5 30.3 - - + -
102A TYR 3.2 8.7 + - - +
103A ALA 3.2 1.0 - - - -
104A ASN* 1.3 80.1 - - - +
106A VAL* 1.4 62.8 + - - +
108A ASN* 4.0 10.0 - - - +
109A ASN* 5.2 2.1 + - - +
114A PHE* 3.7 12.9 - - + -
291B ASP 3.4 24.6 - - - +
292B GLY 3.9 15.0 - - - +
293B GLN* 4.1 11.4 - - - +
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Residues in contact with VAL 106 (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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101A MET* 3.8 26.0 - - + -
102A TYR 4.2 3.4 - - - +
103A ALA 2.9 7.8 + - - +
105A LEU* 1.4 81.0 - - - +
107A PHE* 1.3 61.7 + - - +
109A ASN 4.6 1.6 + - - -
110A GLY 3.5 9.7 + - - +
111A ILE* 3.6 6.9 - - - -
114A PHE* 3.5 48.5 - - + +
115A TYR* 3.8 21.1 - - + +
126A VAL* 5.0 1.3 - - + -
128A VAL* 4.6 9.4 - - + -
139A PHE* 3.6 30.7 - - + -
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Residues in contact with PHE 107 (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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103A ALA 3.0 13.7 + - - +
104A ASN* 4.2 1.6 - - - +
106A VAL* 1.3 79.1 - - - +
108A ASN* 1.3 72.4 + - - +
110A GLY* 3.0 15.0 + - - -
111A ILE* 4.0 29.2 - - + -
139A PHE* 4.8 1.3 - - + -
11B GLU* 4.4 7.2 - - - -
276B VAL* 3.6 42.0 - - + -
277B GLY* 4.1 7.2 - - - -
278B ILE* 3.7 31.4 - - + -
283B LYS* 3.8 29.6 - - + -
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Residues in contact with ASN 108 (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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104A ASN* 2.8 22.7 + - - +
105A LEU* 4.0 11.2 - - - +
106A VAL 3.4 0.2 - - - -
107A PHE* 1.3 84.3 - - - +
109A ASN* 1.3 95.8 + - - +
110A GLY 3.7 0.2 + - - -
275B ARG* 2.7 48.3 + - - +
276B VAL 5.3 2.0 - - - +
288B GLN* 3.1 10.8 - - - +
290B ALA 3.0 12.3 + - - -
291B ASP 3.5 8.4 + - - +
292B GLY* 3.3 11.8 - - - -
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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