Contacts of the helix formed by residues 95 - 108 (chain A) in PDB entry 5H4G
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG* 4.2 9.9 + - - -
93A THR* 5.0 2.2 - - + +
94A LEU* 1.3 79.0 - - - +
96A MET* 1.3 66.0 + - - +
97A GLU* 3.6 14.8 - - - +
98A ASP* 3.0 38.9 + - - +
99A ILE* 3.1 13.0 + - - +
95B ASP* 6.4 2.2 - - + -
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Residues in contact with MET 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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40A VAL* 4.8 1.6 - - + -
72A LEU* 4.1 7.4 - - + -
84A GLU* 5.3 0.6 - - - -
95A ASP* 1.3 76.3 - - - +
97A GLU* 1.3 63.3 + - - +
99A ILE* 3.3 1.9 + - - +
100A ILE* 3.0 39.0 + - + +
40B VAL* 3.2 51.6 - - + -
43B TYR* 3.6 34.3 - - + +
44B ARG* 5.1 7.2 - - - +
95B ASP* 6.6 0.2 - - - -
96B MET* 3.4 30.3 - - + -
97B GLU* 4.2 16.6 - - + +
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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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10A ASP* 5.4 1.4 - - - +
11A SER* 2.6 39.4 + - - -
40A VAL* 4.0 17.1 - - + +
41A THR* 4.5 4.0 - - - -
44A ARG* 2.8 49.0 + - - +
95A ASP* 3.1 11.6 + - - +
96A MET* 1.3 77.5 - - - +
98A ASP* 1.3 63.5 + - - +
100A ILE* 3.5 1.2 + - - +
101A THR* 2.7 44.9 + - - +
119A ARG* 6.2 0.7 - - - -
96B MET* 3.7 13.1 - - - +
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Residues in contact with ASP 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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94A LEU* 4.0 17.7 - - + +
95A ASP* 3.0 34.0 + - - +
97A GLU* 1.3 83.7 - - - +
99A ILE* 1.3 61.5 + - - +
101A THR* 3.4 3.4 + - - -
102A ALA* 2.9 31.2 + - - +
119A ARG* 2.9 47.6 + - - -
120A TYR* 3.8 20.9 + - + -
123A ILE* 5.0 0.9 - - - -
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Residues in contact with ILE 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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80A ALA* 3.8 34.5 - - + +
83A ILE* 4.5 6.5 - - + -
84A GLU* 4.0 21.1 - - + +
87A LEU* 3.3 34.5 - - + -
94A LEU* 4.1 15.3 - - + +
95A ASP 3.1 13.5 + - - +
96A MET 3.8 5.4 - - - +
98A ASP* 1.3 72.5 - - - +
100A ILE* 1.3 62.7 + - - +
102A ALA* 3.8 4.0 - - - +
103A THR* 2.8 36.2 + - - +
123A ILE* 3.9 12.8 - - + -
43B TYR* 3.9 13.9 - - - +
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Residues in contact with ILE 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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38A SER* 3.7 19.5 - - - +
40A VAL* 3.9 19.3 - - + -
72A LEU* 4.0 31.2 - - + -
76A ILE* 4.5 4.7 - - + -
80A ALA* 3.7 26.9 - - + -
96A MET* 3.0 42.1 + - + +
97A GLU 4.2 1.8 - - - +
99A ILE* 1.3 75.1 - - - +
101A THR* 1.3 61.9 + - - +
103A THR* 3.9 2.4 - - - -
104A THR* 2.7 36.3 + - - +
43B TYR* 4.1 16.8 - - + -
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Residues in contact with THR 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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8A THR* 5.3 3.8 - - + +
9A PHE 4.3 2.7 - - - +
10A ASP* 4.1 15.3 - - + +
38A SER* 4.7 9.4 + - - -
40A VAL* 5.3 0.9 - - - +
41A THR* 3.2 26.6 + - - +
97A GLU* 2.7 33.4 + - - +
98A ASP* 3.7 6.3 - - - -
99A ILE 3.2 0.2 - - - -
100A ILE* 1.3 79.2 - - - +
102A ALA* 1.3 61.3 - - - +
104A THR* 3.4 2.3 + - - -
105A ALA* 3.2 21.8 + - - +
112A LEU* 4.0 29.2 - - + -
120A TYR* 4.5 3.1 - - - +
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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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98A ASP 2.9 18.1 + - - +
99A ILE 3.9 1.3 - - - +
101A THR* 1.3 78.2 - - - +
103A THR* 1.3 62.5 + - - +
105A ALA* 3.3 4.8 + - - +
106A ILE* 3.0 27.4 + - - +
112A LEU* 4.6 2.9 - - - -
120A TYR* 4.2 4.9 - - + -
123A ILE* 3.7 29.4 - - + -
128A LEU* 3.7 27.8 - - + +
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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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76A ILE* 3.5 35.9 - - + +
79A LYS* 3.9 18.6 - - + -
80A ALA* 3.5 27.4 - - - +
83A ILE* 3.6 10.3 - - + +
99A ILE* 2.8 23.3 + - - +
100A ILE* 3.9 3.4 - - - -
102A ALA* 1.3 77.3 - - - +
104A THR* 1.3 57.7 + - - +
106A ILE* 3.3 12.3 + - + +
107A TYR* 2.9 26.6 + - + +
123A ILE* 5.7 0.2 - - - +
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Residues in contact with THR 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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36A ASN 5.3 3.1 - - - +
37A LEU 4.9 0.2 - - - -
38A SER* 3.8 28.0 + - - +
70A VAL* 3.7 40.8 - - + -
71A PRO 5.0 1.2 + - - -
76A ILE* 3.7 22.9 - - + +
100A ILE* 2.7 24.0 + - - +
101A THR 3.8 3.6 - - - -
103A THR* 1.3 74.5 - - - +
105A ALA* 1.3 59.1 + - - +
107A TYR* 3.2 1.3 + - - +
108A THR* 2.9 33.2 + - + +
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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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8A THR* 3.8 19.7 - - + +
101A THR 3.2 11.2 + - - +
102A ALA 3.5 9.0 - - - +
104A THR* 1.3 76.2 - - - +
106A ILE* 1.3 60.0 + - - +
108A THR* 3.8 6.7 - - - -
109A ASN* 3.0 9.0 + - - -
110A SER* 2.9 45.9 + - - +
112A LEU* 4.4 2.5 - - + -
128A LEU* 3.8 16.8 - - + -
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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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79A LYS* 5.3 11.7 - - + -
83A ILE* 4.1 11.2 - - + -
102A ALA 3.0 18.9 + - - +
103A THR* 3.5 8.5 - - + +
105A ALA* 1.3 70.8 - - - +
107A TYR* 1.3 67.2 + - - +
109A ASN* 3.1 13.5 + - - +
123A ILE* 4.0 14.6 - - + -
126A PHE* 3.5 40.8 - - + +
127A GLY* 3.7 9.0 - - - +
128A LEU* 3.5 29.4 - - + +
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Residues in contact with TYR 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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70A VAL* 5.0 2.2 - - + -
73A LEU* 3.6 27.8 - - + +
75A ASP* 4.1 30.7 + - + -
76A ILE* 3.9 26.7 - - + -
103A THR* 2.9 18.4 + - + +
104A THR 3.2 5.6 + - - +
106A ILE* 1.3 80.0 - - - +
108A THR* 1.3 74.1 + - + +
109A ASN 3.3 0.6 + - - -
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Residues in contact with THR 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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6A ASP* 4.6 5.9 - - - +
36A ASN* 3.9 18.2 + - + +
70A VAL* 4.0 27.8 - - + -
104A THR* 2.9 24.9 + - + +
105A ALA* 3.6 1.6 + - - -
107A TYR* 1.3 90.1 - - + +
109A ASN* 1.3 68.6 + - - +
110A SER* 2.8 32.1 + - - -
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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