Contacts of the helix formed by residues 82 - 101 (chain A) in PDB entry 3PL7
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 GLU 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER* 1.3 64.9 + - - +
84A GLU* 3.0 25.7 - - - +
85A ALA* 3.2 38.3 + - - +
86A VAL* 3.6 10.4 + - - +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 6.1 5.2 - - - -
82A GLU* 1.3 84.6 + - - +
84A GLU* 1.3 69.3 + - - +
85A ALA 3.2 0.9 - - - -
86A VAL* 3.3 14.5 + - - +
87A LYS* 3.2 33.0 + - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 5.4 0.3 - - - +
82A GLU* 4.0 22.4 - - - +
83A SER* 1.3 82.8 + - - +
85A ALA* 1.3 58.7 + - - +
87A LYS* 3.5 34.9 + - - +
88A GLN* 3.0 30.1 + - - +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.2 25.4 + - - +
84A GLU* 1.3 78.3 - - - +
86A VAL* 1.3 57.4 + - - +
88A GLN* 4.1 4.9 - - - +
89A ALA* 3.2 28.9 + - - +
192A VAL* 3.5 23.1 - - + +
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Residues in contact with VAL 86 (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 LEU* 4.1 18.4 - - + -
82A GLU 3.7 14.1 - - - +
83A SER* 3.3 12.8 + - - +
84A GLU 3.2 0.2 - - - -
85A ALA* 1.3 75.1 - - - +
87A LYS* 1.3 66.5 + - + +
89A ALA* 3.4 2.3 + - - +
90A LEU* 2.9 23.0 + - - +
188A TRP* 3.6 51.6 - - + +
189A ASP* 5.0 1.3 - - - +
191A PHE* 4.5 1.5 - - + -
192A VAL* 3.7 20.0 - - + -
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Residues in contact with LYS 87 (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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7A GLU* 4.4 19.3 + - - +
8A LEU* 4.4 18.6 - - + +
11A ASP* 3.3 46.6 + - + +
83A SER* 3.2 19.2 + - - +
84A GLU* 3.5 38.2 + - - +
86A VAL* 1.3 76.6 - - - +
88A GLN* 1.3 63.8 + - - +
90A LEU* 3.0 4.2 + - - +
91A ARG* 2.8 30.0 + - + +
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Residues in contact with GLN 88 (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 GLU 3.0 15.8 + - - +
85A ALA* 4.1 5.2 - - - +
87A LYS* 1.3 79.3 - - - +
89A ALA* 1.3 64.2 + - - +
91A ARG* 3.3 26.6 + - - +
92A GLU* 2.9 58.4 + - - +
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Residues in contact with ALA 89 (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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85A ALA 3.2 18.2 + - - +
86A VAL 3.7 2.2 - - - +
88A GLN* 1.3 76.9 - - - +
90A LEU* 1.3 58.4 + - - +
92A GLU* 3.2 11.1 + - - +
93A ALA* 2.8 31.4 + - - +
191A PHE* 3.6 23.0 - - + -
192A VAL* 4.3 8.1 - - + -
195A TYR 4.4 3.1 - - - +
196A GLY* 4.1 23.1 - - - -
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Residues in contact with LEU 90 (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 LEU* 3.4 31.0 - - + -
12A PHE* 3.4 23.9 - - + -
86A VAL 2.9 17.7 + - - +
87A LYS* 3.5 4.9 - - - +
89A ALA* 1.3 73.8 - - - +
91A ARG* 1.3 65.4 + - - +
93A ALA* 3.8 0.7 - - - +
94A GLY 2.9 19.8 + - - -
140A ILE* 5.4 0.7 - - + -
141A VAL* 4.4 14.4 - - + +
144A PHE* 3.7 47.1 - - + -
188A TRP* 4.3 10.3 - - + -
191A PHE* 3.6 23.7 - - + -
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.1 45.4 + - - +
12A PHE* 4.2 10.7 - - + -
14A SER* 5.1 3.4 - - - -
15A TYR* 3.5 60.7 - - + +
16A LYS* 4.2 1.0 + - - -
87A LYS* 2.8 21.2 + - - +
88A GLN* 3.4 30.5 - - - +
90A LEU* 1.3 71.9 - - - +
92A GLU* 1.3 60.2 + - + +
94A GLY* 3.4 1.0 + - - -
95A ASP* 2.9 35.2 + - - +
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Residues in contact with GLU 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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88A GLN* 2.9 49.7 + - - +
89A ALA* 3.6 9.9 - - - +
91A ARG* 1.3 74.7 - - + +
93A ALA* 1.3 62.1 + - - +
95A ASP* 3.3 10.2 + - - +
96A GLU* 3.0 28.5 + - - +
195A TYR 5.0 3.9 - - - +
196A GLY* 4.5 15.1 - - - -
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Residues in contact with ALA 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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89A ALA 2.8 20.4 + - - +
90A LEU 3.8 3.8 - - - +
92A GLU* 1.3 74.0 - - - +
94A GLY* 1.3 56.2 + - - +
96A GLU* 3.2 11.2 + - - +
97A PHE* 2.9 29.8 + - - +
141A VAL* 4.0 17.7 - - + +
191A PHE* 3.9 20.6 - - + -
195A TYR* 4.2 18.7 + - + +
70C LEU* 4.4 4.6 - - + +
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Residues in contact with GLY 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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12A PHE* 4.1 11.7 - - - -
16A LYS* 4.0 1.8 - - - -
90A LEU 2.9 16.7 + - - -
91A ARG 3.8 1.3 - - - -
93A ALA* 1.3 75.8 - - - +
95A ASP* 1.3 57.8 + - - +
97A PHE* 3.3 2.6 - - - +
98A GLU* 3.0 39.8 + - - +
141A VAL* 4.2 5.3 - - - +
145A SER* 3.9 16.6 - - - -
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Residues in contact with ASP 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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15A TYR* 2.5 28.4 + - - -
16A LYS* 2.5 28.2 + - - +
19A GLN* 3.1 13.6 + - - -
91A ARG 2.9 15.9 + - - +
92A GLU* 3.5 13.6 - - - +
94A GLY* 1.3 76.0 - - - +
96A GLU* 1.3 57.6 + - - +
98A GLU* 3.2 5.7 + - - +
99A LEU* 2.9 42.6 + - + +
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Residues in contact with GLU 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 GLU 3.0 14.1 + - - +
93A ALA* 3.2 12.5 + - - +
95A ASP* 1.3 76.1 - - - +
97A PHE* 1.3 64.0 + - - +
99A LEU* 3.1 10.2 + - - +
100A ARG* 2.6 69.2 + - + +
70C LEU* 3.8 18.3 - - + +
74C MET* 3.4 28.8 - - - +
77C GLN* 5.6 0.3 + - - -
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Residues in contact with PHE 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 ALA 2.9 13.1 + - - +
94A GLY* 3.3 10.8 - - - +
96A GLU* 1.3 77.6 - - - +
98A GLU* 1.3 62.1 + - - +
101A TYR* 3.1 30.9 + + - +
105A PHE* 3.1 34.5 - + - -
138A GLY 4.8 0.2 - - - -
141A VAL* 4.2 8.3 - - + -
142A ALA* 3.8 24.7 - - + -
145A SER* 3.3 26.2 - - - +
63C LEU* 4.7 4.5 - - + -
66C ILE* 2.9 42.2 - - + -
67C GLY* 3.8 15.9 - - - -
70C LEU* 3.8 25.7 - - + +
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Residues in contact with GLU 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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12A PHE* 4.4 0.3 - - - -
16A LYS* 3.3 38.0 + - - +
19A GLN* 4.5 1.7 - - - +
94A GLY 3.0 16.8 + - - +
95A ASP* 3.2 4.2 + - - +
97A PHE* 1.3 76.3 - - - +
99A LEU* 1.3 57.4 + - + +
101A TYR 3.6 0.5 - - - +
102A ARG* 3.1 31.5 + - - +
105A PHE* 3.7 42.9 - - + +
145A SER* 3.3 27.1 + - - +
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Residues in contact with LEU 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 ASP* 2.9 29.9 + - + +
96A GLU* 3.5 8.3 - - - +
98A GLU* 1.3 75.4 - - + +
100A ARG* 1.3 68.1 + - + +
101A TYR 3.1 2.7 + - - -
102A ARG* 3.4 34.6 + - + +
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Residues in contact with ARG 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 GLU* 2.6 52.1 + - + +
99A LEU* 1.3 75.5 - - + +
101A TYR* 1.3 70.3 + - + +
102A ARG 3.6 0.8 + - - -
100B ARG* 2.8 69.3 + - + +
101B TYR* 3.5 37.3 - - - -
103B ARG* 4.6 12.3 - - - +
70C LEU* 4.0 8.0 - - - +
73C ASN* 4.1 9.1 - - - +
77C GLN* 4.9 0.4 - - - +
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Residues in contact with TYR 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 PHE* 3.1 19.5 + - - +
98A GLU 3.6 3.8 - - - -
99A LEU 3.1 0.4 - - - -
100A ARG* 1.3 86.6 - - + +
102A ARG* 1.3 62.2 + - - +
103A ARG 3.2 3.1 + - - -
104A ALA* 3.4 8.1 + - + +
105A PHE* 3.0 25.5 + - + +
100B ARG* 3.4 38.4 - - - +
101B TYR* 3.0 31.9 + - - -
65C ARG* 6.2 0.9 - - - -
66C ILE* 3.2 59.9 - - + -
69C GLU* 2.8 33.0 + - - +
70C LEU* 4.6 7.0 - - + -
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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