Contacts of the helix formed by residues 92 - 107 (chain A) in PDB entry 1PJR
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 PHE 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.8 19.5 - - + +
63A THR 3.5 10.9 + - - -
64A PHE* 3.9 26.9 - + - +
91A THR* 1.3 72.4 - - - +
93A HIS* 1.3 65.9 + - + +
95A MET* 3.6 4.9 - - + +
96A CYS* 3.3 29.7 + - - -
196A ILE* 4.2 14.6 - - + -
222A ILE* 3.4 33.7 - - + -
228A THR* 4.3 4.3 - - - -
232A GLN* 3.6 54.5 - - + +
235A LEU* 4.1 18.4 - - + -
236A VAL* 3.8 15.0 - - + -
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Residues in contact with HIS 93 (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 THR* 3.2 7.0 + - - +
92A PHE* 1.3 77.9 - - + +
94A SER* 1.3 65.6 + - - +
96A CYS* 3.2 5.0 + - - +
97A VAL* 2.9 28.9 + - + +
192A PHE* 3.7 53.4 + + + +
193A ASP* 5.5 1.8 - - - -
195A LEU* 4.0 17.5 - - + +
196A ILE* 4.7 15.8 - - + +
232A GLN* 6.1 1.6 - - - -
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Residues in contact with SER 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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66A ASN* 4.6 9.2 + - - -
90A SER* 3.7 18.8 - - - -
91A THR* 2.8 23.2 + - - -
93A HIS* 1.3 78.0 - - - +
95A MET* 1.3 61.2 - - - +
97A VAL* 3.4 8.0 + - - +
98A ARG* 3.2 23.5 + - - +
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Residues in contact with MET 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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60A LEU* 4.1 28.3 - - + -
62A ILE* 4.5 14.6 - - + -
88A TRP* 3.9 19.2 - - + -
90A SER* 3.7 17.2 + - - +
91A THR 3.2 12.0 + - - +
92A PHE* 3.6 12.6 - - + +
94A SER* 1.3 78.1 - - - +
96A CYS* 1.3 62.3 + - - +
98A ARG* 3.2 5.3 + - - +
99A ILE* 2.9 45.2 + - + +
217A PHE* 5.0 1.6 - - - -
235A LEU* 3.5 34.8 - - + -
239A LEU* 3.9 21.8 - - + -
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Residues in contact with CYS 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 PHE 3.3 18.0 + - - +
93A HIS* 3.2 5.0 + - - +
95A MET* 1.3 81.3 - - - +
97A VAL* 1.3 60.7 + - - +
99A ILE* 3.2 4.9 + - - +
100A LEU* 2.9 31.7 + - - +
195A LEU* 3.6 20.4 - - + +
196A ILE* 4.2 9.2 - - - -
199A THR* 3.4 30.3 - - + -
235A LEU* 3.8 26.9 - - - -
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Residues in contact with VAL 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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93A HIS 2.9 20.4 + - - +
94A SER* 3.7 7.6 - - - +
96A CYS* 1.3 73.1 - - - +
98A ARG* 1.3 59.7 + - + +
100A LEU* 3.3 4.5 + - - +
101A ARG* 2.9 54.3 + - + +
113A PHE* 4.9 2.7 - - + -
115A ILE* 4.1 16.6 - - + -
195A LEU* 3.8 28.5 - - + -
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Residues in contact with ARG 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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86A ASP* 5.6 4.8 + - - +
87A VAL 5.3 1.4 + - - -
88A TRP* 3.5 66.4 - - + +
90A SER* 5.6 3.4 + - - -
94A SER 3.2 10.9 + - - +
95A MET* 3.2 10.5 + - - +
97A VAL* 1.3 83.5 - - - +
99A ILE* 1.3 60.1 + - - +
101A ARG* 4.0 5.3 + - - +
102A ARG* 3.9 17.5 + - - +
213A TYR* 4.6 1.9 + - - -
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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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88A TRP* 4.4 7.4 - - + -
95A MET* 2.9 45.6 + - + +
96A CYS* 3.7 8.1 - - - +
98A ARG* 1.3 74.0 - - - +
100A LEU* 1.3 63.1 + - - +
102A ARG* 3.4 12.1 + - - +
103A ASP* 3.5 13.5 + - - +
199A THR* 4.3 11.7 - - - +
202A LEU* 4.1 19.2 - - + +
203A PHE* 4.1 27.4 - - + -
209A VAL* 4.9 0.2 - - + -
213A TYR* 3.9 45.1 + - + -
217A PHE* 5.0 3.8 - - + -
239A LEU* 5.6 1.1 - - + -
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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 CYS 2.9 20.0 + - - +
97A VAL 3.7 0.7 - - - +
99A ILE* 1.3 71.3 - - - +
101A ARG* 1.3 57.7 + - - +
102A ARG 2.8 11.1 + - - -
104A ILE* 2.8 50.2 + - + +
113A PHE* 3.6 20.2 - - + -
190A LEU* 3.6 31.0 - - + -
195A LEU* 4.1 23.1 - - + +
198A THR* 4.2 5.4 - - + -
199A THR* 3.8 23.3 - - + +
202A LEU* 4.0 20.9 - - + -
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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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97A VAL* 2.9 36.2 + - + +
98A ARG* 4.4 5.4 - - - +
99A ILE 3.5 0.6 - - - -
100A LEU* 1.3 69.0 - - - +
102A ARG* 1.3 57.2 + - - +
111A ARG* 2.6 57.4 + - - +
112A ASN* 3.4 5.3 - - - +
113A PHE* 2.9 55.7 + - + +
114A SER* 4.9 1.0 - - - +
115A ILE* 4.2 15.4 - - - +
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Residues in contact with ARG 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 ARG 3.9 9.6 + - - +
99A ILE 3.4 7.8 + - - +
100A LEU 2.8 3.2 + - - -
101A ARG* 1.3 76.6 - - - +
103A ASP* 1.3 89.3 + - - +
104A ILE 3.9 0.4 - - - -
105A ASP* 3.6 0.5 - - - +
106A ARG* 4.8 4.2 - - - +
111A ARG* 3.2 26.6 + - - +
212A TYR* 3.7 38.8 + - - -
213A TYR* 3.4 19.5 + - - -
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Residues in contact with ASP 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 ILE 3.5 6.6 + - - +
100A LEU 3.2 1.2 + - - -
102A ARG* 1.3 116.6 + - - +
104A ILE* 1.4 62.6 + - - +
105A ASP* 3.1 8.6 - - - +
106A ARG* 2.7 58.8 + - - +
202A LEU* 3.5 11.8 - - + +
209A VAL* 4.1 27.6 - - + +
212A TYR* 5.4 0.2 - - - -
213A TYR* 4.3 4.3 + - - -
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Residues in contact with ILE 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 51.2 + - + +
102A ARG 3.9 0.4 - - - -
103A ASP* 1.4 70.9 - - - +
105A ASP* 1.3 65.3 + - - +
107A ILE* 3.0 32.1 + - + +
108A GLY 3.5 2.4 + - - -
109A ILE* 3.4 42.4 + - + +
110A ASN 3.8 13.7 - - - +
111A ARG* 3.8 10.1 - - + +
113A PHE* 4.0 8.1 - - + -
190A LEU* 4.3 8.3 - - + -
198A THR* 3.7 24.2 - - + -
202A LEU* 4.7 4.5 - - - -
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Residues in contact with ASP 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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102A ARG 3.6 7.3 - - - +
103A ASP* 3.6 5.9 - - - +
104A ILE* 1.3 80.0 - - - +
106A ARG* 1.3 71.4 + - - +
108A GLY* 3.1 14.4 + - - -
109A ILE 3.2 13.0 - - - +
110A ASN* 5.6 0.7 - - - -
111A ARG* 3.2 46.5 + - + +
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Residues in contact with ARG 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 ARG* 4.8 4.8 - - - +
103A ASP* 2.7 47.4 + - - +
104A ILE 3.0 0.4 + - - -
105A ASP* 1.3 88.1 + - - +
107A ILE* 1.3 59.7 + - - +
202A LEU* 4.6 0.2 - - + -
206A VAL* 3.9 40.3 - - + +
208A ASP* 4.7 12.3 + - - +
209A VAL* 3.8 12.6 - - - +
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Residues in contact with ILE 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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104A ILE* 3.0 26.4 + - + +
106A ARG* 1.3 81.4 - - - +
108A GLY* 1.3 59.3 + - - +
109A ILE* 4.4 11.8 - - + +
198A THR* 4.0 27.4 - - + +
201A GLN* 4.8 10.5 - - + +
202A LEU* 4.3 23.8 - - + +
205A ARG* 4.2 37.6 + - + +
206A VAL* 4.2 13.5 - - + -
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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