Contacts of the helix formed by residues 97 - 113 (chain A) in PDB entry 6P7B
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 SER 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLY 3.7 4.2 - - - +
96A GLY* 1.3 78.0 - - - +
98A TYR* 1.3 64.6 + - - +
99A ARG* 3.9 5.8 + - - +
100A ASN* 2.2 54.8 + - - +
101A ARG* 3.6 4.7 + - - +
29F T 6.0 1.1 - - - -
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Residues in contact with TYR 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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96A GLY 3.8 0.8 + - - -
97A SER* 1.3 74.1 - - - +
99A ARG* 1.3 77.0 + - + +
101A ARG* 3.2 31.7 + - + +
102A LYS* 3.7 8.3 + - + +
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Residues in contact with ARG 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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97A SER* 3.3 6.1 + - - +
98A TYR* 1.3 88.6 - - + +
100A ASN* 1.3 65.5 + - - +
102A LYS* 3.1 44.3 + - - +
103A LYS* 3.2 50.2 + - + +
129A LYS* 5.2 4.0 - - - +
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Residues in contact with ASN 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 GLY 5.2 1.8 - - - +
96A GLY* 4.8 4.3 - - - -
97A SER* 2.2 43.0 + - - +
99A ARG* 1.3 78.2 - - - +
101A ARG* 1.3 60.8 + - - +
103A LYS* 4.5 6.1 - - - +
104A GLN* 3.1 31.3 + - - +
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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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60A GLU* 2.6 36.5 + - - -
91A PRO* 4.6 1.9 - - - +
92A THR* 4.2 17.6 + - - +
93A PHE* 3.0 46.3 + - + +
94A LYS* 6.2 0.2 - - - -
95A GLY 5.4 4.5 - - - +
97A SER 3.6 4.4 + - - +
98A TYR* 3.2 25.1 + - + +
99A ARG 3.1 0.8 - - - -
100A ASN* 1.3 77.2 - - - +
102A LYS* 1.3 57.2 + - - +
104A GLN* 3.9 4.8 - - - +
105A SER* 2.7 38.1 + - - -
135A ASN* 2.9 44.6 + - - +
139A LEU* 6.1 0.6 - - - +
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Residues in contact with LYS 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 TYR* 3.7 7.6 + - + +
99A ARG* 3.1 45.8 + - - +
101A ARG* 1.3 80.7 - - - +
103A LYS* 1.3 78.2 + - + +
105A SER* 3.2 5.0 + - - -
106A ILE* 2.9 50.5 + - - +
129A LYS* 3.9 17.7 - - - +
130A LEU 5.3 0.8 - - - +
131A ASP* 3.3 45.9 + - + +
135A ASN* 5.7 0.9 - - - -
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Residues in contact with LYS 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 ARG* 3.2 47.6 + - + +
100A ASN* 4.5 6.3 - - - +
102A LYS* 1.3 94.3 - - + +
104A GLN* 1.3 58.6 + - - +
106A ILE* 3.2 21.8 - - + +
107A ASP* 2.9 31.5 + - - +
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Residues in contact with GLN 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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93A PHE* 4.2 33.2 - - + +
100A ASN* 3.1 23.5 + - - +
101A ARG* 3.9 2.9 - - - +
103A LYS* 1.3 76.8 - - - +
105A SER* 1.3 62.4 + - - +
107A ASP* 3.3 6.4 + - + +
108A VAL* 3.0 28.5 + - + +
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Residues in contact with SER 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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93A PHE* 3.3 19.3 - - - -
101A ARG* 2.7 24.1 + - - -
102A LYS* 3.5 6.1 - - - -
104A GLN* 1.3 74.4 - - - +
106A ILE* 1.3 58.4 + - - +
108A VAL 3.4 0.2 + - - -
109A PHE* 2.9 29.6 + - - +
131A ASP* 5.8 1.1 - - - -
134A ALA* 3.3 11.2 - - - +
135A ASN* 2.9 26.2 + - - -
138A ASN* 3.0 20.8 + - - -
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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 LYS* 2.9 24.4 + - - +
103A LYS* 3.2 39.3 - - + +
105A SER* 1.3 76.3 - - - +
107A ASP* 1.3 61.4 + - + +
109A PHE* 3.6 1.3 - - - +
110A ILE* 2.9 44.2 + - + +
130A LEU* 3.6 36.1 - - + +
131A ASP* 3.7 19.5 - - + -
134A ALA* 3.9 7.6 - - + -
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Residues in contact with ASP 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 LYS 2.9 19.5 + - - +
104A GLN* 3.6 7.6 - - - +
106A ILE* 1.3 76.0 - - + +
108A VAL* 1.3 67.5 + - - +
110A ILE* 3.3 7.6 + - - +
111A GLN* 2.9 37.2 + - - +
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Residues in contact with VAL 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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93A PHE* 3.9 15.9 - - + -
104A GLN* 3.0 18.2 + - + +
107A ASP* 1.3 75.4 - - - +
109A PHE* 1.3 59.0 + - - +
111A GLN* 3.3 26.0 - - - +
112A LYS* 2.9 52.2 + - + +
137A PHE* 5.9 0.2 - - + -
138A ASN* 3.2 30.1 - - - +
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Residues in contact with PHE 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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32A ILE* 4.0 11.2 - - + -
105A SER 2.9 18.8 + - - +
106A ILE 3.6 2.9 - - - +
108A VAL* 1.3 80.2 - - - +
110A ILE* 1.3 75.0 + - + +
113A ILE* 2.9 60.0 + - + +
123A ILE* 4.2 15.7 - - + -
124A LEU* 5.2 4.3 - - + -
130A LEU* 4.7 13.2 - - + -
133A ILE* 3.8 37.5 - - + -
134A ALA* 3.5 27.1 - - + -
137A PHE* 3.7 32.3 - + + -
138A ASN* 4.5 3.8 - - - +
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Residues in contact with ILE 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 ILE* 2.9 30.7 + - + +
107A ASP* 3.8 8.1 - - - +
109A PHE* 1.3 77.1 - - + +
111A GLN* 1.3 63.9 + - + +
113A ILE* 3.3 26.1 - - - +
114A SER* 4.4 0.5 + - - -
120A LYS* 4.0 21.8 + - - +
124A LEU* 4.8 14.1 - - + -
130A LEU* 3.8 30.1 - - + -
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Residues in contact with GLN 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 ASP* 2.9 30.5 + - - +
108A VAL* 3.3 35.6 - - - +
110A ILE* 1.3 81.1 - - + +
112A LYS* 1.3 69.1 + - + +
113A ILE 3.6 0.4 - - - -
114A SER* 4.8 7.5 + - - -
115A GLU* 4.6 7.8 - - - +
120A LYS* 5.7 1.1 - - - +
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Residues in contact with LYS 112 (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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108A VAL* 2.9 38.3 + - + +
109A PHE 3.7 0.7 - - - +
111A GLN* 1.3 88.9 - - + +
113A ILE* 1.3 62.1 + - - +
114A SER 3.3 2.4 + - - -
115A GLU* 3.8 24.7 + - - +
116A TYR* 3.0 42.7 + - - -
137A PHE* 4.2 9.9 - - + -
138A ASN* 6.1 0.2 - - - -
141A LEU* 3.7 25.3 - - - +
145A GLU* 4.7 7.5 + - - -
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Residues in contact with ILE 113 (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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32A ILE* 5.2 3.1 - - + -
109A PHE* 2.9 62.3 + - + +
110A ILE* 3.3 20.9 - - - +
112A LYS* 1.3 78.7 - - - +
114A SER* 1.3 86.9 + - - +
116A TYR* 2.9 17.4 + - + +
117A THR* 3.2 23.6 + - + +
120A LYS* 3.5 39.9 - - + +
123A ILE* 5.3 4.3 - - + -
124A LEU* 5.1 4.5 - - + -
137A PHE* 4.4 14.1 - - + -
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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