Contacts of the helix formed by residues 95 - 112 (chain A) in PDB entry 4B18
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A SER* 3.4 3.0 + - - -
94A LYS* 1.3 78.4 - - - +
96A PRO* 1.3 68.2 - - - +
97A GLU* 3.2 14.2 + - - +
98A GLN* 3.2 39.2 + - - +
99A GLN* 2.8 28.1 + - - +
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Residues in contact with PRO 96 (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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94A LYS* 3.5 9.8 - - - +
95A SER* 1.3 82.9 - - - +
97A GLU* 1.3 81.5 + - - +
99A GLN* 3.3 13.5 + - - +
100A LEU* 3.0 24.4 + - - +
137A ARG* 3.9 16.8 - - - +
140A ASN* 4.7 13.7 + - - +
143A LEU* 4.7 2.4 - - - +
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Residues in contact with GLU 97 (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 SER* 3.2 8.9 + - - +
96A PRO* 1.3 97.1 - - - +
98A GLN* 1.3 60.3 + - + +
100A LEU* 3.4 9.0 + - - +
101A SER* 2.9 28.8 + - - -
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Residues in contact with GLN 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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89A GLU* 6.0 1.8 - - - +
90A MET* 3.5 49.1 - - + +
93A SER* 3.5 28.4 + - - +
95A SER* 3.2 19.4 + - - +
97A GLU* 1.3 74.4 - - + +
99A GLN* 1.3 67.4 + - - +
101A SER* 3.6 6.6 - - - -
102A ALA* 3.0 19.9 + - - +
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Residues in contact with GLN 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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90A MET 3.7 14.1 - - - +
91A ILE* 4.1 1.2 - - - +
93A SER 2.8 28.1 + - - +
94A LYS 4.0 7.0 + - - -
95A SER 2.8 28.3 + - - +
96A PRO* 3.5 5.2 - - - +
98A GLN* 1.3 77.4 - - - +
100A LEU* 1.3 53.3 + - - +
102A ALA* 3.6 2.9 + - - +
103A THR* 2.7 37.3 + - - -
130A ARG* 3.0 14.1 - - - +
134A PHE* 3.7 22.2 - - + -
137A ARG* 2.4 47.6 + - - +
143A LEU* 3.9 4.7 - - + +
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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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96A PRO 3.0 16.4 + - - +
97A GLU* 3.7 7.4 - - - +
99A GLN* 1.3 74.8 - - - +
101A SER* 1.3 61.6 + - - +
103A THR* 3.1 2.5 + - - -
104A GLN* 2.8 46.7 + - - +
140A ASN* 5.6 4.9 - - - +
142A THR* 4.0 24.2 - - + -
143A LEU* 3.5 42.6 - - + +
146A GLU* 4.0 15.0 - - + -
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Residues in contact with SER 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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90A MET* 4.9 9.1 - - - -
97A GLU 2.9 17.9 + - - -
98A GLN* 3.3 9.4 + - - -
100A LEU* 1.3 74.6 - - - +
102A ALA* 1.3 63.6 + - - +
104A GLN* 3.1 25.8 + - - +
105A LYS* 3.1 22.7 + - - +
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Residues in contact with ALA 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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87A MET* 3.6 33.7 - - + +
90A MET* 3.7 9.9 - - + +
91A ILE* 3.7 19.3 - - + +
98A GLN 3.0 16.2 + - - +
99A GLN 3.9 0.7 - - - +
101A SER* 1.3 77.6 - - - +
103A THR* 1.3 61.2 + - - +
105A LYS* 3.1 10.6 + - - +
106A PHE* 2.9 29.0 + - - -
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Residues in contact with THR 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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91A ILE* 4.6 0.9 - - - +
99A GLN 2.7 23.9 + - - -
100A LEU* 3.1 8.9 + - - -
102A ALA* 1.3 76.5 - - - +
104A GLN* 1.3 57.5 + - - +
106A PHE* 3.4 7.1 + - - +
107A ARG* 2.8 26.5 + - - +
131A PHE* 3.9 18.0 - - + -
134A PHE* 3.4 20.4 - - - -
143A LEU* 4.0 3.8 - - + +
146A GLU* 3.6 29.2 - - + +
147A SER* 3.9 20.2 - - - +
150A VAL* 4.0 2.0 - - + +
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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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100A LEU* 2.8 37.8 + - - +
101A SER* 3.5 17.0 + - - +
103A THR* 1.3 74.5 - - - +
105A LYS* 1.3 60.2 + - - +
107A ARG* 2.9 13.3 + - - +
108A LYS* 2.8 50.9 + - + +
142A THR* 4.6 5.0 - - - +
146A GLU* 3.7 32.0 - - + +
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Residues in contact with LYS 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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84A THR* 5.5 3.4 - - - +
87A MET* 4.0 35.2 - - + -
90A MET* 5.8 6.3 - - - -
101A SER* 3.1 20.1 + - - -
102A ALA* 3.1 10.2 + - - +
104A GLN* 1.3 75.9 - - - +
106A PHE* 1.3 65.8 + - - +
108A LYS* 3.1 8.0 + - - +
109A LEU* 2.9 35.7 + - + +
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Residues in contact with PHE 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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83A ILE* 5.2 6.3 - - + -
87A MET* 3.8 39.2 - - + +
88A ILE* 4.5 10.5 - - + -
91A ILE* 3.2 31.9 - - + -
102A ALA 2.9 25.4 + - - -
103A THR 3.4 7.0 - - - +
105A LYS* 1.3 76.2 - - - +
107A ARG* 1.3 62.1 + - - +
109A LEU* 3.3 4.7 + - + +
110A LEU* 3.0 31.6 + - + +
121A VAL* 3.9 33.2 - - + -
127A VAL* 4.0 19.5 - - + -
131A PHE* 3.5 29.4 - + + -
150A VAL* 4.0 7.2 - - + -
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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 THR 2.8 19.9 + - - +
104A GLN* 2.9 13.0 + - - +
106A PHE* 1.3 73.1 - - - +
108A LYS* 1.3 88.2 + - - +
110A LEU* 3.3 5.2 + - - +
111A SER* 2.5 35.5 + - - -
145A PHE* 5.6 0.2 - - - -
146A GLU* 2.5 44.5 + - - +
149A TRP* 3.5 63.5 + - + -
150A VAL* 3.6 16.2 - - + +
241B ALA 5.2 5.7 + - - -
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Residues in contact with LYS 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 GLN* 2.8 36.7 + - - +
105A LYS* 3.9 5.6 - - - +
107A ARG* 1.3 104.8 - - - +
109A LEU* 1.3 63.6 + - + +
111A SER* 2.9 24.8 + - - -
112A LYS* 3.4 7.3 + - - +
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Residues in contact with LEU 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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82A VAL 4.4 17.3 - - - +
83A ILE* 5.0 2.5 - - + -
87A MET* 4.0 28.5 - - + -
105A LYS* 2.9 26.9 + - + +
106A PHE* 3.8 4.7 - - + +
108A LYS* 1.3 77.9 - - + +
110A LEU* 1.3 59.6 + - + +
112A LYS* 3.4 43.7 - - + +
116A PRO* 3.8 0.2 - - - +
117A PRO* 3.1 38.0 - - + +
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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 PHE* 3.0 25.1 + - + +
107A ARG* 3.7 4.0 - - - +
109A LEU* 1.3 76.8 - - - +
111A SER* 1.3 60.8 + - - +
112A LYS 3.3 1.7 - - - +
116A PRO* 3.6 18.8 - - + +
117A PRO* 4.2 30.3 - - + +
118A ILE* 4.2 18.2 - - + -
121A VAL* 4.2 16.6 - - + -
150A VAL* 3.8 40.8 - - + +
153A ASN* 3.1 28.5 + - + +
154A ILE* 4.3 12.6 - - + +
238B PRO* 5.7 1.4 - - - +
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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* 2.5 32.8 + - - -
108A LYS* 2.9 16.3 + - - +
110A LEU* 1.3 78.0 - - - +
112A LYS* 1.3 62.1 + - - +
113A GLU 3.4 1.6 + - - -
149A TRP* 4.0 7.4 + - - -
153A ASN* 4.2 6.5 - - - +
239B ARG 4.2 5.2 - - - -
240B ARG* 3.3 22.7 - - - +
241B ALA* 3.9 25.1 + - - -
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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 LYS 3.4 7.1 + - - +
109A LEU* 3.4 45.4 - - + +
110A LEU 3.3 1.1 - - - +
111A SER* 1.3 75.9 - - - +
113A GLU* 1.3 67.5 + - - +
114A PRO* 3.6 13.9 - - + -
115A ASN 4.7 9.2 - - - +
116A PRO* 3.5 26.5 - - + +
117A PRO* 5.1 3.4 - - + -
240B ARG* 4.5 3.3 + - - -
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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