Contacts of the helix formed by residues 97 - 111 (chain A) in PDB entry 5HZZ
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ALA* 5.1 1.6 - - - +
27A GLU 5.9 0.2 + - - -
95A GLY 3.9 2.4 + - - -
96A ILE* 1.3 69.0 - - - +
98A ALA* 1.3 64.1 + - - +
99A ASP* 3.0 25.9 + - - +
100A ALA* 3.3 24.0 + - + +
101A VAL* 3.3 14.9 + - - +
141A LEU* 3.7 28.7 - - + +
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Residues in contact with ALA 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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11A ALA* 4.0 8.9 - - + +
88A TYR* 3.7 31.6 - - + +
91A LEU* 3.6 34.5 - - + +
96A ILE* 3.0 7.4 + - - +
97A ASP* 1.3 73.6 + - - +
99A ASP* 1.3 58.2 + - - +
101A VAL* 3.3 6.5 + - - +
102A PHE* 2.8 31.4 + - - +
10C ASN* 5.1 0.2 - - - -
81C ALA* 5.5 0.3 - - - +
84C LEU* 4.4 3.0 - - + +
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Residues in contact with ASP 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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9A THR* 2.7 39.4 + - - +
11A ALA* 3.5 15.7 - - - +
12A GLU* 4.8 4.5 - - - +
88A TYR* 4.4 0.9 + - - -
97A ASP* 3.0 10.3 + - - +
98A ALA* 1.3 78.1 - - - +
100A ALA* 1.3 57.0 + - - +
102A PHE* 3.8 5.9 - - - +
103A ALA* 2.9 30.5 + - - +
10C ASN* 3.0 28.5 + - - +
13C ARG* 5.4 4.5 + - - +
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Residues in contact with ALA 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 ASP* 3.3 25.7 + - - +
99A ASP* 1.3 80.2 - - - +
101A VAL* 1.3 61.1 + - - +
103A ALA* 3.5 5.5 + - - +
104A GLU* 3.5 16.8 + - - +
137A VAL* 3.8 24.9 - - + +
140A ARG* 5.2 11.4 - - - +
141A LEU* 4.0 12.1 - - + -
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Residues in contact with VAL 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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91A LEU* 5.4 3.1 - - + -
96A ILE* 3.6 30.3 - - + -
97A ASP 3.3 4.7 + - - +
98A ALA* 3.3 7.5 + - - +
100A ALA* 1.3 76.5 - - - +
102A PHE* 1.3 63.7 + - - +
104A GLU* 3.2 6.1 + - - +
105A VAL* 3.0 20.4 + - - +
134A VAL* 4.0 24.0 - - + -
137A VAL* 4.0 18.6 - - + -
138A ILE* 4.5 9.0 - - + -
141A LEU* 4.6 0.4 - - + -
77C ALA* 3.7 15.3 - - + +
81C ALA* 3.6 22.7 - - + -
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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 ALA 2.8 22.3 + - - +
99A ASP 3.8 4.0 - - - +
101A VAL* 1.3 74.5 - - - +
103A ALA* 1.3 57.0 + - - +
105A VAL* 3.3 5.1 + - + +
106A HIS* 2.7 27.4 + - + +
10C ASN* 3.1 53.6 - - + +
13C ARG* 3.9 16.4 - - + -
14C LEU* 3.6 15.9 - - + -
81C ALA* 4.1 10.9 - - + +
84C LEU* 3.8 35.4 - - + -
85C TYR* 3.4 40.8 - + - -
88C TYR* 4.0 8.1 - + - -
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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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99A ASP 2.9 17.4 + - - +
100A ALA* 3.9 6.5 - - - +
101A VAL 3.3 0.4 - - - -
102A PHE* 1.3 76.7 - - - +
104A GLU* 1.3 57.7 + - - +
106A HIS* 3.7 8.4 - - - +
107A ARG* 3.1 28.8 + - - +
13C ARG* 4.2 24.4 - - - +
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Residues in contact with GLU 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 ALA 3.5 3.5 + - - +
101A VAL* 3.2 9.5 + - - +
103A ALA* 1.3 76.3 - - - +
105A VAL* 1.3 64.5 + - - +
107A ARG* 2.9 36.7 + - - +
108A ALA* 3.3 16.8 + - - +
131A PRO 5.0 0.2 - - - +
132A ALA* 3.6 14.6 - - + +
133A ASP* 2.9 51.8 + - - +
134A VAL* 4.4 3.6 - - + +
137A VAL* 3.7 22.3 - - + +
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Residues in contact with VAL 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 VAL 3.0 16.5 + - - +
102A PHE* 3.7 4.3 - - - +
104A GLU* 1.3 74.6 - - - +
106A HIS* 1.3 63.3 + - - +
108A ALA* 3.2 4.5 + - - +
109A ASN* 3.0 36.3 + - - +
132A ALA* 4.0 7.0 - - + -
134A VAL* 4.2 11.4 - - + -
78C HIS* 3.9 26.2 - - + +
81C ALA* 3.8 20.2 - - + +
82C ASP* 3.4 25.1 - - - +
85C TYR* 4.2 10.1 - - + -
201C UMP 3.7 1.6 - - - +
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Residues in contact with HIS 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* 2.7 21.7 + - + +
103A ALA 3.7 5.8 - - - +
105A VAL* 1.3 73.3 - - - +
107A ARG* 1.3 63.8 + - - +
109A ASN* 2.9 11.3 + - - -
110A LEU* 2.9 44.7 + - + +
13C ARG* 3.1 60.4 + - + +
16C GLU* 2.9 23.0 + - - -
17C PHE* 4.1 0.2 - - + -
85C TYR* 2.7 40.1 + - + -
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Residues in contact with ARG 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 3.1 16.9 + - - +
104A GLU* 2.9 36.5 + - - +
105A VAL 3.3 0.2 - - - -
106A HIS* 1.3 79.9 - - + +
108A ALA* 1.3 60.4 + - - +
110A LEU* 3.5 12.5 + - + +
111A SER* 3.3 21.7 + - - -
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Residues in contact with ALA 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 GLU* 3.3 8.5 + - - +
105A VAL 3.2 9.0 + - - +
106A HIS 3.2 0.6 - - - -
107A ARG* 1.3 78.5 - - - +
109A ASN* 1.3 59.9 + - - +
111A SER* 3.1 9.2 + - - -
112A LYS* 3.6 2.3 - - - +
129A TRP* 2.8 39.8 + - + -
130A ARG 4.3 3.8 - - - +
131A PRO 4.2 2.0 - - - -
132A ALA* 3.6 32.3 - - + +
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Residues in contact with ASN 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 VAL* 3.0 18.1 + - - +
106A HIS 2.9 8.5 + - - +
108A ALA* 1.3 78.9 - - - +
110A LEU* 1.3 66.3 + - - +
111A SER 3.1 1.6 - - - -
112A LYS* 2.9 45.6 + - - +
113A ALA 4.3 0.7 + - - -
129A TRP* 5.1 0.7 - - - -
17C PHE* 3.3 25.6 - - + -
21C ILE* 5.1 0.2 - - - +
85C TYR* 3.4 37.0 - - - +
201C UMP 3.1 34.5 + - - +
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Residues in contact with LEU 110 (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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106A HIS* 2.9 52.9 + - + +
107A ARG* 3.5 10.3 + - + +
109A ASN* 1.3 76.0 - - - +
111A SER* 1.3 59.8 + - - +
112A LYS 3.1 1.4 + - - -
113A ALA* 3.3 21.2 + - - +
16C GLU* 3.8 27.8 - - + +
17C PHE* 3.7 24.9 - - - -
20C ALA* 4.3 10.9 - - + +
21C ILE* 6.1 0.2 - - - -
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Residues in contact with SER 111 (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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107A ARG 3.3 10.7 + - - -
108A ALA* 3.1 11.0 + - - -
109A ASN 3.1 0.2 - - - -
110A LEU* 1.3 76.9 - - - +
112A LYS* 1.3 59.2 + - - +
113A ALA 3.3 1.5 + - - -
114A SER* 4.7 2.4 + - - -
126A PRO* 3.7 14.9 - - - +
129A TRP* 3.1 27.7 + - - -
130A ARG 4.9 1.7 + - - -
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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