Contacts of the helix formed by residues 99 - 109 (chain A) in PDB entry 6UZA
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 GLU 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ARG* 5.3 2.8 + - - -
95A LEU* 3.8 23.5 - - + +
96A SER* 3.5 29.1 + - - -
97A ILE 3.4 0.2 - - - -
98A GLU* 1.3 81.4 - - - +
100A GLU* 1.3 60.6 + - - +
101A ARG 3.2 0.9 - - - -
102A PHE* 3.3 5.9 + - - +
103A LEU* 2.9 32.6 + - - +
123A SER 5.1 3.6 - - - +
124A LEU* 4.3 11.3 - - + +
125A ASN* 4.0 19.5 + - - +
128A CYS* 3.7 27.6 - - - +
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Residues in contact with GLU 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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95A LEU* 4.5 18.7 - - + +
96A SER 3.2 17.6 + - - +
97A ILE* 4.5 4.5 - - + +
99A GLU* 1.3 75.1 - - - +
101A ARG* 1.3 58.2 + - + +
103A LEU* 3.9 4.9 - - - +
104A ASP* 2.9 40.6 + - - +
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Residues in contact with ARG 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 ILE* 3.4 23.1 + - + +
98A GLU* 4.7 6.0 - - - +
99A GLU 3.2 0.4 - - - -
100A GLU* 1.3 78.6 - - - +
102A PHE* 1.3 56.1 + - - +
104A ASP* 3.4 5.3 + - - +
105A ALA* 2.9 30.8 + - - +
113A VAL* 3.9 18.6 - - + +
116A LYS* 3.1 28.3 - - - +
117A MET* 3.4 34.3 - - + +
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Residues in contact with PHE 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 GLU 4.2 4.3 - - - +
99A GLU* 3.3 9.8 + - - +
101A ARG* 1.3 78.4 - - - +
103A LEU* 1.3 59.3 + - + +
105A ALA* 3.4 2.3 + - + +
106A ALA* 2.9 29.8 + - + +
114A VAL* 4.1 26.9 - - + -
117A MET* 3.7 35.9 - - + +
118A LEU* 3.8 30.5 - - + -
124A LEU* 4.3 16.6 - - + -
125A ASN 4.8 0.2 - - - -
126A VAL* 4.3 21.8 - - + -
128A CYS* 4.4 16.2 - - - -
136A ALA* 3.7 23.8 - - + -
152A LEU* 3.9 15.3 - - + -
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Residues in contact with LEU 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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95A LEU* 3.9 24.0 - - + -
99A GLU 2.9 18.3 + - - +
100A GLU* 4.0 4.3 - - - +
101A ARG 3.3 0.2 - - - -
102A PHE* 1.3 75.5 - - + +
104A ASP* 1.3 61.7 - - - +
106A ALA* 3.4 3.0 + - - +
107A GLU* 2.9 31.8 + - - +
128A CYS* 3.8 29.2 - - - +
129A VAL 3.8 28.3 - - - +
130A ASP* 3.9 11.0 - - + +
134A GLN 4.4 1.1 - - - +
135A ASN 4.3 1.1 - - - -
136A ALA* 4.2 21.8 - - + +
139A LEU* 4.0 19.6 - - + +
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Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLU* 2.9 25.9 + - - +
101A ARG* 3.9 5.6 - - - +
103A LEU* 1.3 78.8 - - - +
105A ALA* 1.3 57.7 + - - +
107A GLU* 4.6 3.7 - - - +
108A TYR* 2.9 56.9 + - + +
175D ARG* 5.6 4.2 + - - +
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Residues in contact with ALA 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 ARG 2.9 19.0 + - - +
102A PHE* 3.8 4.3 - - + +
104A ASP* 1.3 76.0 - - - +
106A ALA* 1.3 61.0 + - - +
109A GLY 3.3 2.8 + - - -
110A ASN* 2.9 43.0 + - + +
113A VAL* 3.8 22.2 - - + -
114A VAL* 3.8 19.5 - - + -
148A ILE* 3.6 5.2 - - - +
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Residues in contact with ALA 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 PHE* 2.9 20.3 + - + +
103A LEU* 3.9 4.0 - - - +
104A ASP 3.3 0.2 - - - -
105A ALA* 1.3 77.2 - - - +
107A GLU* 1.3 63.4 + - - +
114A VAL* 4.1 5.8 - - + +
136A ALA* 3.7 37.2 - - + +
139A LEU* 4.8 3.1 - - + -
140A ALA* 3.9 10.9 - - - +
145A HIS* 3.6 15.1 - - - -
148A ILE* 3.9 19.8 - - + +
152A LEU* 5.1 0.7 - - + -
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Residues in contact with GLU 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 LEU 2.9 17.8 + - - +
104A ASP* 4.1 5.8 - - - +
106A ALA* 1.3 79.4 - - - +
108A TYR* 1.3 93.0 + - + +
130A ASP* 5.6 1.0 - - - +
139A LEU* 4.2 29.6 - - + +
143A ASN* 3.4 29.9 + - - +
145A HIS* 3.0 17.8 + - - -
889A GLN* 3.4 5.5 - - - +
233D GLU* 5.5 5.2 - - - +
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Residues in contact with TYR 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 ASP* 2.9 42.6 + - + +
107A GLU* 1.3 108.6 + - + +
109A GLY* 1.3 58.5 + - - +
110A ASN* 3.6 2.5 - - + +
145A HIS* 3.8 4.0 + - - -
889A GLN* 3.7 23.2 - - - +
892A SER* 3.0 27.9 + - - +
893A SER 4.5 0.2 + - - -
896A TYR* 3.6 9.4 - - + +
174D VAL* 5.1 8.7 - - - +
175D ARG* 3.7 62.1 - - + +
233D GLU* 5.2 5.2 + - - -
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Residues in contact with GLY 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 ALA 3.3 4.2 + - - -
107A GLU 3.4 3.6 - - - -
108A TYR* 1.3 78.9 - - - +
110A ASN* 1.3 60.1 + - - +
111A ILE* 2.9 18.4 + - - +
145A HIS* 3.5 22.8 + - - -
148A ILE* 3.7 13.0 - - - -
893A SER* 3.7 18.2 - - - +
896A TYR* 4.0 6.6 - - - +
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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