Contacts of the helix formed by residues 95 - 109 (chain A) in PDB entry 1O2D
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 GLY 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLY* 1.3 74.8 - - - -
96A GLY* 1.3 67.1 + - - -
97A SER 3.2 4.1 + - - -
98A PRO* 3.2 6.6 - - - +
99A MSE 3.1 25.9 + - - +
136A THR* 3.7 3.0 + - - -
137A THR* 3.8 15.5 - - - -
1800A NAP 3.3 28.5 + - - -
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Residues in contact with GLY 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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95A GLY* 1.3 72.0 - - - -
97A SER* 1.3 57.2 + - - +
99A MSE 3.8 8.2 - - - +
100A ASP* 2.8 35.1 + - - -
140A THR* 3.6 17.1 + - - -
142A SER* 4.5 3.4 - - - -
1800A NAP 2.9 34.6 + - - -
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Residues in contact with SER 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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66A VAL* 3.9 3.6 - - - -
67A GLU 3.6 20.0 - - - -
68A GLU* 4.1 2.0 - - - -
69A ASN 2.9 19.9 + - - -
70A PRO* 3.5 15.2 - - - +
96A GLY* 1.3 76.6 - - - +
98A PRO* 1.3 67.2 - - - +
100A ASP* 3.8 0.8 - - - +
101A PHE* 3.0 27.4 + - - +
1800A NAP 2.7 38.6 + - - -
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Residues in contact with PRO 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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34A VAL* 3.5 12.8 - - - +
35A THR* 3.8 20.6 - - - +
36A GLY* 4.2 9.0 - - - +
66A VAL* 3.8 14.8 - - + +
92A GLY* 4.1 2.2 - - - -
93A LEU 3.4 26.5 - - - +
94A GLY* 3.7 1.8 - - - -
95A GLY 3.2 20.4 - - - +
97A SER* 1.3 94.7 - - - +
99A MSE 1.3 55.5 + - - +
101A PHE* 3.5 3.9 - - + +
102A ALA* 2.9 24.9 + - - +
1800A NAP 3.6 10.1 - - - +
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Residues in contact with MSE 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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92A GLY* 4.2 10.1 - - - +
94A GLY 3.6 21.3 - - - +
95A GLY* 3.1 25.4 + - - +
96A GLY 3.8 0.7 - - - +
98A PRO* 1.3 77.4 - - - +
100A ASP* 1.3 62.9 + - - +
102A ALA* 3.4 7.6 + - - +
103A LYS* 3.4 6.4 + - - +
133A GLU* 2.7 48.0 - - - +
135A PRO* 3.6 35.9 - - + -
137A THR* 5.2 3.4 - - - +
140A THR* 3.7 19.7 - - - +
141A GLY 5.3 0.2 - - - +
142A SER* 3.7 13.7 - - - +
143A GLU* 3.8 23.3 - - - +
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Residues in contact with ASP 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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70A PRO* 5.3 1.1 - - + -
96A GLY 2.8 21.3 + - - +
97A SER* 3.8 3.1 - - - +
99A MSE 1.3 73.2 - - - +
101A PHE* 1.3 66.7 + - - +
103A LYS* 3.2 6.2 + - - +
104A ALA 3.2 12.3 + - - -
142A SER* 2.7 30.1 + - - -
147A TYR 3.6 0.9 - - - +
148A SER* 2.9 30.2 + - - +
149A ILE* 3.0 30.9 + - - +
150A LEU* 5.1 1.8 - - + -
1800A NAP 2.8 36.6 + - - -
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Residues in contact with PHE 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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34A VAL* 4.1 11.7 - - + -
63A PHE* 3.5 23.8 - + - -
66A VAL* 3.8 16.6 - - + -
70A PRO* 3.8 20.8 - - + +
74A ASN* 3.4 48.2 - - - -
75A VAL* 3.6 15.3 - - + -
78A ALA* 3.6 21.8 - - + -
97A SER 3.0 17.5 + - - +
98A PRO* 3.5 10.1 - - + +
100A ASP* 1.3 78.0 - - - +
102A ALA* 1.3 61.3 + - - +
104A ALA* 3.2 6.9 + - - +
105A VAL* 3.0 39.9 + - + +
150A LEU* 5.0 4.5 - - - -
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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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34A VAL* 3.6 19.0 - - + +
90A VAL* 3.8 15.5 - - + +
92A GLY* 3.7 21.1 - - - +
98A PRO 2.9 16.3 + - - +
99A MSE 3.5 6.7 - - - +
100A ASP 3.2 0.4 - - - -
101A PHE* 1.3 77.8 - - - +
103A LYS* 1.3 57.5 + - - +
105A VAL* 3.8 1.5 - - - -
106A ALA* 2.9 30.7 + - - +
131A VAL* 4.3 7.0 - - + -
133A GLU* 4.1 4.7 - - - +
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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 MSE 3.6 4.3 - - - +
100A ASP* 3.2 7.3 + - - +
102A ALA* 1.3 76.0 - - - +
104A ALA* 1.3 64.5 + - - +
106A ALA 3.4 0.2 + - - -
107A VAL* 3.4 19.6 + - - +
131A VAL* 4.2 7.2 - - + -
133A GLU* 3.3 24.2 - - - +
142A SER* 2.8 33.2 + - - -
145A THR* 2.8 31.0 + - - +
146A PRO 4.2 2.2 - - - +
147A TYR 2.8 31.6 + - - +
148A SER* 4.4 0.9 - - - -
162A LEU* 3.6 10.9 - - + +
163A MSE 3.4 41.5 - - - +
165A PRO* 4.3 5.2 - - + -
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Residues in contact with ALA 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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75A VAL* 4.3 13.9 - - + -
100A ASP 3.2 10.0 + - - +
101A PHE* 3.7 7.9 - - - +
103A LYS* 1.3 80.4 - - - +
105A VAL* 1.3 63.5 + - - +
107A VAL* 3.3 5.0 + - - +
108A LEU* 3.1 27.3 + - - +
119A LEU* 3.8 20.4 - - + -
148A SER* 4.1 8.5 - - - +
150A LEU* 4.3 12.3 - - + -
162A LEU* 3.7 11.3 - - + +
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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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32A LEU* 3.7 19.1 - - + -
34A VAL* 5.2 1.1 - - + -
75A VAL* 4.5 5.6 - - + -
78A ALA* 4.5 5.4 - - + -
79A VAL* 3.9 24.7 - - + -
82A TYR* 5.8 0.2 - - + -
90A VAL* 4.6 5.8 - - + -
101A PHE* 3.0 46.6 + - + +
102A ALA* 4.0 4.3 - - - +
104A ALA* 1.3 74.5 - - - +
106A ALA* 1.3 57.1 + - - +
109A LEU* 2.8 60.4 + - + +
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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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90A VAL* 3.9 18.8 - - + +
102A ALA 2.9 10.5 + - - +
104A ALA 3.3 0.4 - - - -
105A VAL* 1.3 77.9 - - - +
107A VAL* 1.3 62.6 + - - +
110A LYS* 3.8 2.8 + - - +
128A TRP* 3.6 1.3 - - - -
129A LEU* 3.0 45.1 + - + +
131A VAL* 3.3 33.7 - - + -
163A MSE 3.7 6.5 - - + -
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Residues in contact with VAL 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 3.4 6.9 + - - +
104A ALA 3.3 6.6 + - - +
105A VAL 3.2 0.6 - - - -
106A ALA* 1.3 76.5 - - - +
108A LEU* 1.3 59.0 + - - +
110A LYS* 3.1 4.7 + - - +
111A GLU* 2.9 35.8 + - + +
114A LEU* 4.3 8.5 - - + -
119A LEU* 3.6 22.4 - - + -
125A VAL* 4.1 24.0 - - + -
127A HIS 3.9 10.8 - - - +
128A TRP* 4.0 10.5 - - + -
162A LEU* 4.2 15.3 - - + -
163A MSE 3.6 22.9 - - + -
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Residues in contact with LEU 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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75A VAL* 3.8 28.5 - - + -
79A VAL* 3.8 21.1 - - + -
83A ARG* 2.8 32.4 + - - +
104A ALA 3.1 18.4 + - - +
105A VAL 4.1 0.2 - - - +
107A VAL* 1.3 76.5 - - + +
109A LEU* 1.3 62.2 + - - +
111A GLU 3.2 8.7 - - - +
114A LEU* 3.8 27.6 - - + +
115A SER 3.6 20.9 - - - +
116A VAL* 4.0 17.3 - - + +
119A LEU* 3.9 21.8 - - + -
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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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32A LEU* 3.9 15.5 - - + -
79A VAL* 4.3 11.0 - - + +
82A TYR* 3.7 33.7 - - + +
83A ARG* 3.7 15.5 - - + +
87A PHE* 4.1 18.8 - - + -
90A VAL* 4.4 3.6 - - + -
105A VAL* 2.8 43.7 + - + +
108A LEU* 1.3 77.2 - - - +
110A LYS* 1.3 59.3 + - - +
112A LYS* 3.6 24.5 - - - -
129A LEU* 4.1 24.5 - - + -
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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