Contacts of the helix formed by residues 91 - 104 (chain A) in PDB entry 1PTG
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 LEU 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.2 22.0 - - + -
78A ILE* 3.1 46.8 + - + +
80A LEU* 4.1 10.8 - - + +
90A THR* 1.3 70.8 - - - +
92A HIS* 1.3 68.7 + - - +
94A PHE* 2.8 19.8 + - + +
95A ILE* 3.0 26.7 + - + +
112A MET* 4.3 11.9 - - - -
114A LEU* 5.1 4.9 - - + -
132A PHE* 3.8 29.8 - - + -
136A TYR* 3.9 21.8 - - + -
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Residues in contact with HIS 92 (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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77A THR* 5.1 9.9 - - + +
78A ILE 4.8 0.2 + - - -
90A THR* 3.4 8.7 + - - +
91A LEU* 1.3 76.6 - - - +
93A GLU* 1.3 63.2 + - - +
95A ILE* 3.2 9.3 + - + +
96A ASN* 3.0 40.6 + - - +
135A LYS* 4.7 7.1 + - + -
136A TYR* 3.1 44.8 + + - -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 5.0 3.1 - - - -
38A LYS* 2.7 35.5 + - - -
55A PHE* 4.9 4.4 - - + -
88A TYR 4.3 0.3 - - - +
89A VAL* 3.5 15.2 - - + +
90A THR* 3.3 34.8 + - - +
91A LEU 3.1 0.4 - - - -
92A HIS* 1.3 78.7 - - - +
94A PHE* 1.3 62.8 + - - +
96A ASN* 3.7 7.0 + - - +
97A GLU* 3.2 32.7 + - + +
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Residues in contact with PHE 94 (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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55A PHE* 3.7 36.9 - + + -
59A MET* 4.0 10.1 - - + -
66A PHE* 3.7 36.6 - + + -
68A ILE* 4.0 11.0 - - + -
80A LEU* 5.1 2.0 - - + -
90A THR 3.4 5.5 + - - +
91A LEU* 2.8 21.2 + - + +
93A GLU* 1.3 73.8 - - - +
95A ILE* 1.3 70.3 + - + +
96A ASN 2.9 1.7 + - - -
97A GLU* 2.9 14.2 + - - +
98A ALA* 3.0 16.2 + - + +
110A ILE* 3.1 32.5 - - + -
112A MET* 3.6 40.8 - - + -
158A ILE* 4.9 4.0 - - + -
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Residues in contact with ILE 95 (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* 3.0 30.1 + - + +
92A HIS* 3.9 8.7 - - + +
94A PHE* 1.3 84.7 - - + +
96A ASN* 1.3 61.1 + - - +
98A ALA* 3.9 6.0 - - - +
99A LYS* 3.0 47.8 + - - +
112A MET* 4.9 0.7 - - - -
132A PHE* 5.2 0.2 - - + -
136A TYR* 3.7 32.1 - - + -
139A ASP* 4.8 1.3 - - - +
141A ILE* 3.9 17.7 - - + -
142A PHE* 3.9 25.6 - - + -
158A ILE* 4.3 5.2 - - + -
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Residues in contact with ASN 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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92A HIS* 3.0 35.5 + - - +
93A GLU* 4.1 6.4 - - - +
94A PHE 2.9 0.2 + - - -
95A ILE* 1.3 75.0 - - - +
97A GLU* 1.3 63.4 + - + +
99A LYS* 3.0 25.3 + - - +
100A GLN* 2.9 37.5 + - + +
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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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54A ASP* 4.9 8.0 - - - +
55A PHE* 4.2 28.9 + - + +
56A ARG* 3.7 29.5 + - + +
59A MET* 4.2 5.1 - - + +
93A GLU* 3.2 21.1 + - + +
94A PHE 2.9 7.4 + - - +
96A ASN* 1.3 78.0 - - - +
98A ALA* 1.3 57.1 + - - +
100A GLN* 3.3 9.9 + - - +
101A PHE* 2.9 31.9 + - - +
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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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59A MET* 3.6 14.7 - - + +
94A PHE* 3.0 17.4 + - + +
95A ILE 3.9 2.2 - - - +
97A GLU* 1.3 78.3 - - - +
99A LYS* 1.3 52.3 + - - +
101A PHE* 3.8 0.4 - - - +
102A LEU* 2.8 43.2 + - + +
110A ILE* 3.7 23.1 - - + -
158A ILE* 3.7 26.7 - - + -
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Residues in contact with LYS 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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95A ILE* 3.0 30.5 + - + +
96A ASN* 3.0 24.4 + - - +
98A ALA* 1.3 75.8 - - - +
100A GLN* 1.3 68.9 + - - +
102A LEU* 3.6 6.0 - - - +
103A LYS* 2.8 32.1 + - - +
139A ASP* 2.8 28.7 + - - -
141A ILE* 3.4 34.5 - - + -
158A ILE* 5.3 1.8 - - + -
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Residues in contact with GLN 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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56A ARG* 3.7 10.3 - - - +
96A ASN* 2.9 24.8 + - + +
97A GLU* 3.9 10.3 - - - +
99A LYS* 1.3 78.9 - - - +
101A PHE* 1.3 69.7 + - - +
103A LYS* 3.1 31.0 + - - +
104A ASP* 3.0 27.0 + - - +
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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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11A SER* 3.4 22.0 - - - -
56A ARG* 3.2 29.1 - - - +
59A MET* 3.5 46.7 - - + -
60A ASP* 3.9 9.2 - - - -
64A ARG* 3.6 21.5 - - - -
97A GLU 2.9 17.9 + - - +
98A ALA 3.8 2.2 - - - +
100A GLN* 1.3 79.1 - - - +
102A LEU* 1.3 68.5 + - + +
104A ASP* 3.1 0.7 + - - +
105A ASN* 2.9 51.4 + - - -
108A GLU* 3.6 23.3 - - + -
110A ILE* 4.5 10.5 - - + -
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Residues in contact with LEU 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 36.1 + - + +
99A LYS* 3.9 7.0 - - - +
100A GLN 3.3 0.2 - - - -
101A PHE* 1.3 79.4 - - + +
103A LYS* 1.3 57.1 + - - +
105A ASN 3.9 2.7 - - - -
106A PRO* 3.2 27.7 - - - +
108A GLU* 3.6 26.2 - - + +
109A THR* 3.7 19.5 - - - +
110A ILE* 4.2 11.4 - - + -
141A ILE* 4.7 4.7 - - + -
156A GLY* 3.9 23.6 - - - +
157A LYS 3.9 10.1 - - - +
158A ILE* 3.8 27.4 - - + -
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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 LYS 2.8 24.4 + - - +
100A GLN* 3.1 34.3 + - - +
102A LEU* 1.3 73.6 - - - +
104A ASP* 1.3 79.3 + - - +
105A ASN 3.2 0.4 - - - -
106A PRO* 3.5 11.5 - - - +
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Residues in contact with ASP 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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12A LYS* 4.2 6.2 - - - -
56A ARG* 3.4 27.5 + - - +
100A GLN* 3.0 16.9 + - - +
101A PHE 3.6 4.0 - - - +
103A LYS* 1.3 98.4 + - - +
105A ASN* 1.3 74.8 + - - +
106A PRO* 3.4 4.7 - - - +
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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