Contacts of the helix formed by residues 99 - 109 (chain A) in PDB entry 5UAK
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 PRO 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LYS 3.6 6.3 - - - +
96A ALA* 3.2 16.4 - - - +
97A VAL 3.3 1.8 - - - -
98A GLN* 1.4 93.0 - - + +
100A LEU* 1.3 63.2 + - - +
102A LEU* 3.5 21.5 - - + +
103A GLY* 3.5 2.3 + - - -
338A THR* 3.1 21.8 + - - +
341A SER* 3.2 42.6 - - - +
342A PHE* 3.7 22.0 - - + -
345A VAL* 5.9 0.2 - - + -
1137A MET* 5.4 2.2 - - - -
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Residues in contact with LEU 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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97A VAL* 3.5 28.0 - - + +
98A GLN 3.2 1.0 + - - -
99A PRO* 1.3 75.1 - - - +
101A LEU* 1.3 68.4 + - + +
103A GLY* 2.9 22.7 + - - -
104A ARG* 3.5 9.2 + - - +
214A LEU* 3.7 30.1 - - + -
342A PHE* 3.8 16.2 - - + -
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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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97A VAL* 5.0 8.1 - - + +
98A GLN 3.5 5.0 + - - +
99A PRO 3.5 0.2 - - - -
100A LEU* 1.3 84.3 - - + +
102A LEU* 1.3 63.9 + - - +
104A ARG* 3.7 10.5 + - + +
105A ILE* 3.4 25.3 + - - +
123A LEU* 3.6 48.3 - - + +
126A GLY* 4.6 3.6 - - - -
127A LEU* 3.7 32.7 - - + +
130A LEU* 5.8 4.0 - - + -
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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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99A PRO* 3.5 16.6 + - + +
100A LEU 3.1 0.4 - - - -
101A LEU* 1.3 76.7 - - - +
103A GLY* 1.3 64.9 + - - +
105A ILE* 2.9 16.6 + - + +
106A ILE* 3.0 44.3 + - + +
127A LEU* 4.0 4.0 - - - +
337A PHE* 5.4 0.9 - - + -
338A THR* 4.6 10.1 - - - +
341A SER* 3.7 24.9 - - - +
1133A LEU* 3.8 20.2 - - + -
1134A THR* 4.0 22.0 - - + -
1137A MET* 3.7 41.3 - - + -
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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 PRO 3.5 5.8 + - - -
100A LEU 2.9 11.4 + - - -
102A LEU* 1.3 80.5 - - - +
104A ARG* 1.3 51.7 + - - +
106A ILE* 3.5 6.0 + - - +
107A ALA* 2.8 35.4 + - - +
334A ARG* 4.0 20.2 - - - -
338A THR* 5.1 9.2 + - - -
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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 LEU 3.5 10.9 + - - +
101A LEU* 4.0 5.4 - - + +
102A LEU 3.2 0.6 - - - -
103A GLY* 1.3 74.1 - - - +
105A ILE* 1.3 57.3 + - + +
107A ALA* 3.2 9.2 + - - +
108A SER* 2.8 33.6 + - - -
119A ILE* 5.7 1.1 - - - +
120A ALA* 6.2 0.7 - - - -
123A LEU* 3.5 38.4 - - + +
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Residues in contact with ILE 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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101A LEU 3.4 15.9 + - - +
102A LEU* 2.9 9.5 + - + +
104A ARG* 1.3 78.0 - - + +
106A ILE* 1.3 61.5 + - - +
108A SER* 3.5 17.3 - - - -
109A TYR* 4.0 12.1 - - + -
120A ALA* 3.4 45.8 - - + +
123A LEU* 4.9 2.7 - - + -
124A GLY* 4.5 10.1 - - - +
127A LEU* 6.0 3.1 - - + -
1119A ILE* 4.0 28.0 - - + -
1129A VAL* 4.2 6.4 - - + +
1133A LEU* 3.5 29.6 - - + -
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Residues in contact with ILE 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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102A LEU* 3.0 44.8 + - + +
103A GLY* 3.9 7.6 - - - +
105A ILE* 1.3 75.1 - - - +
107A ALA* 1.3 60.9 + - - +
108A SER 3.3 0.7 + - - -
109A TYR* 3.6 14.6 + - - +
110A ASP* 3.4 10.8 - - - +
334A ARG* 3.5 35.0 - - + +
337A PHE* 4.7 17.3 - - + -
1126A GLU* 5.1 10.4 - - + +
1129A VAL* 4.6 5.6 - - + -
1130A GLY* 3.7 26.0 - - - +
1133A LEU* 3.8 18.8 - - + -
1134A THR* 5.7 0.9 - - + -
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Residues in contact with ALA 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 GLY 2.8 20.1 + - - +
104A ARG* 3.2 13.2 + - - +
106A ILE* 1.3 76.9 - - - +
108A SER* 1.3 64.1 + - - +
110A ASP* 3.6 21.4 - - - +
112A ASP* 4.9 2.9 - - - +
115A GLU* 5.7 0.7 - - - +
334A ARG* 4.4 19.7 - - - +
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Residues in contact with SER 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 ARG 2.8 11.9 + - - -
105A ILE* 3.5 15.7 - - - -
106A ILE 3.2 0.2 - - - -
107A ALA* 1.3 78.8 - - - +
109A TYR* 1.3 73.4 + - - +
110A ASP 3.1 11.6 + - - +
113A ASN 5.6 1.7 - - - +
115A GLU* 4.8 16.6 + - - +
116A GLU 4.9 2.1 + - - -
117A ARG* 5.8 0.7 - - - -
119A ILE* 4.1 21.1 - - - +
120A ALA* 4.4 13.1 - - - +
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Residues in contact with TYR 109 (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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105A ILE* 4.0 15.9 - - + -
106A ILE 3.6 7.7 + - - +
107A ALA 3.5 0.2 - - - -
108A SER* 1.3 84.5 - - - +
110A ASP* 1.3 71.0 + - - +
117A ARG* 5.7 4.2 - - - +
120A ALA* 5.6 2.0 - - + -
1118A SER 5.2 1.6 - - - -
1119A ILE* 2.7 41.3 + - + +
1121A THR 4.3 6.1 + - - -
1122A THR* 6.2 0.2 - - - -
1123A GLY* 4.0 25.6 - - - -
1124A GLU 5.9 1.3 - - - +
1125A GLY 4.9 7.2 - - - +
1126A GLU* 3.7 16.7 - - - +
1129A VAL* 4.1 29.2 - - + -
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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