Contacts of the helix formed by residues 3 - 19 (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 GLN 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 1.3 61.8 + - - +
5A ASN* 3.0 20.0 - - - +
6A ARG* 3.4 19.3 + - - +
7A GLU* 2.9 25.3 - - - +
175A ASN* 4.4 12.9 + - - +
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Residues in contact with SER 4 (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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3A GLN* 1.3 77.8 - - - +
5A ASN* 1.3 65.0 + - - +
6A ARG 3.3 0.2 - - - -
7A GLU* 3.3 13.2 + - - +
8A LEU* 2.9 28.6 + - - +
83A SER* 6.1 5.6 - - - -
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Residues in contact with ASN 5 (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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3A GLN 3.0 6.1 - - - +
4A SER* 1.3 83.2 + - - +
6A ARG* 1.3 63.6 + - - +
8A LEU* 3.5 8.8 - - - +
9A VAL* 3.1 28.9 + - - +
171A ALA* 5.0 2.2 - - - +
174A LEU* 3.8 25.7 - - + +
175A ASN* 2.5 39.6 + - - +
179A GLU* 3.1 33.1 + - - +
188A TRP* 4.2 16.5 + - - -
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Residues in contact with ARG 6 (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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3A GLN* 3.4 18.5 + - - +
4A SER 3.3 0.2 - - - -
5A ASN* 1.3 77.8 - - - +
7A GLU* 1.3 66.3 + - - +
9A VAL* 3.4 3.8 + - + +
10A VAL* 3.1 43.4 + - + +
171A ALA* 4.3 21.9 - - + +
175A ASN* 5.5 1.3 - - - +
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Residues in contact with GLU 7 (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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3A GLN 2.9 22.5 - - - +
4A SER* 3.5 13.7 - - - +
5A ASN 3.2 0.2 - - - -
6A ARG* 1.3 83.8 + - + +
8A LEU* 1.3 59.0 + - - +
10A VAL* 3.5 6.1 + - - +
11A ASP* 2.9 31.4 + - - +
87A LYS* 4.4 14.7 + - - +
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Residues in contact with LEU 8 (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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4A SER 2.9 14.7 + - - +
5A ASN* 3.5 16.6 - - - +
7A GLU* 1.3 74.8 - - - +
9A VAL* 1.3 61.9 + - - +
11A ASP* 3.1 7.1 + - + +
12A PHE* 3.1 22.5 + - + +
86A VAL* 4.1 15.9 - - + -
87A LYS* 4.4 29.8 - - + +
90A LEU* 3.4 23.3 - - + -
144A PHE* 4.3 9.9 - - + -
174A LEU* 4.9 1.6 - - + -
188A TRP* 3.6 44.0 - - + +
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Residues in contact with VAL 9 (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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5A ASN 3.1 13.4 + - - +
6A ARG* 3.6 10.3 - - - +
8A LEU* 1.3 79.4 - - - +
10A VAL* 1.3 62.6 + - + +
12A PHE* 3.6 1.2 + - - +
13A LEU* 3.1 49.3 + - + +
143A PHE* 5.6 0.2 - - + -
144A PHE* 3.9 22.9 - - + -
167A ALA* 3.5 27.4 - - + +
170A MET* 4.1 13.2 - - + +
171A ALA* 4.1 22.0 - - + +
174A LEU* 4.2 9.0 - - + -
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Residues in contact with VAL 10 (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 ARG* 3.1 30.2 + - + +
7A GLU* 3.5 6.5 + - - +
9A VAL* 1.3 79.8 - - + +
11A ASP* 1.3 57.7 + - - +
13A LEU* 4.0 4.4 - - - +
14A SER* 2.9 38.1 + - - +
24A TRP* 3.4 50.6 - - + +
167A ALA* 5.2 2.7 - - + -
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Residues in contact with ASP 11 (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 2.9 19.0 + - - +
8A LEU* 3.4 5.5 - - + +
10A VAL* 1.3 77.9 - - - +
12A PHE* 1.3 64.3 + - - +
14A SER* 3.5 4.8 - - - -
15A TYR* 3.0 21.7 + - - +
84A GLU* 5.4 0.5 - - - +
87A LYS* 3.3 48.9 + - + +
91A ARG* 3.1 36.7 + - - +
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Residues in contact with PHE 12 (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* 3.1 15.9 + - + +
9A VAL 4.0 2.7 - - - +
11A ASP* 1.3 79.6 + - - +
13A LEU* 1.3 66.0 + - + +
15A TYR* 3.2 7.7 + + - +
16A LYS* 2.9 61.5 + - + +
90A LEU* 3.4 48.2 - - + -
91A ARG* 4.2 7.2 - - - -
94A GLY* 4.1 6.3 - - - -
141A VAL* 5.2 0.9 - - + -
144A PHE* 3.1 58.6 - + + -
145A SER* 3.8 15.5 - - - -
148A GLY* 4.7 1.1 - - - -
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Residues in contact with LEU 13 (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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9A VAL* 3.1 29.2 + - + +
10A VAL 4.0 2.7 - - - +
12A PHE* 1.3 79.6 - - + +
14A SER* 1.3 60.8 + - - +
16A LYS* 3.8 3.1 - - - +
17A LEU* 2.9 36.8 + - + +
24A TRP* 4.1 14.6 - - + -
147A GLY 3.8 31.0 - - - +
148A GLY* 3.9 9.0 - - - +
151A CYS* 3.9 21.1 - - + -
167A ALA* 3.6 38.1 - - + +
170A MET* 4.1 14.4 - - + -
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Residues in contact with SER 14 (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 VAL* 2.9 24.2 + - - +
11A ASP* 3.5 7.2 - - - -
13A LEU* 1.3 75.3 - - - +
15A TYR* 1.3 53.6 + - - +
17A LEU* 3.2 3.0 + - - +
18A SER* 2.7 39.0 + - - -
22A TYR 4.9 0.3 - - - +
24A TRP* 3.1 38.5 + - - +
91A ARG* 5.1 4.0 - - - -
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Residues in contact with TYR 15 (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 ASP 3.0 11.8 + - - +
12A PHE* 3.2 7.8 + - - +
14A SER* 1.3 79.6 - - - +
16A LYS* 1.3 76.4 + - - +
18A SER* 3.1 14.0 + - - -
19A GLN* 3.0 56.7 + - + +
91A ARG* 3.5 62.3 - - + +
95A ASP* 2.5 35.2 + - - -
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Residues in contact with LYS 16 (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* 2.9 54.9 + - + +
13A LEU 4.0 3.6 - - - +
15A TYR* 1.3 89.0 - - - +
17A LEU* 1.3 66.6 + - + +
19A GLN* 3.0 29.7 + - - +
20A LYS* 3.7 13.0 + - - +
91A ARG 4.6 0.7 - - - -
94A GLY 4.7 0.4 - - - -
95A ASP* 2.5 39.0 + - - +
98A GLU* 3.3 27.7 + - - +
148A GLY* 4.4 18.2 - - - -
152A VAL* 4.1 10.8 - - + +
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Residues in contact with LEU 17 (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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13A LEU* 2.9 22.1 + - + +
14A SER* 3.6 3.8 - - - +
16A LYS* 1.3 75.2 - - - +
18A SER* 1.3 63.9 + - - +
20A LYS* 3.0 10.0 + - - +
22A TYR* 3.0 55.9 + - + +
24A TRP* 4.0 37.5 - - + +
27A PHE* 4.5 5.4 - - + -
151A CYS* 4.4 10.8 - - + -
152A VAL* 4.4 19.7 - - + +
155A VAL* 4.0 19.1 - - + -
163A VAL* 4.2 14.8 - - + -
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Residues in contact with SER 18 (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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14A SER 2.7 21.4 + - - -
15A TYR* 3.1 19.5 + - - -
17A LEU* 1.3 72.8 - - - +
19A GLN* 1.3 62.5 + - - +
20A LYS 3.1 1.0 + - - -
21A GLY* 3.1 12.4 + - - -
22A TYR 3.3 13.0 + - - +
23A SER* 6.1 0.2 - - - -
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Residues in contact with GLN 19 (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* 3.0 42.8 + - + +
16A LYS* 3.0 40.3 + - - +
17A LEU 3.1 1.0 - - - -
18A SER* 1.3 79.1 + - - +
20A LYS* 1.3 68.2 + - + +
21A GLY 3.4 1.1 - - - -
95A ASP* 3.1 21.8 + - - -
98A GLU* 4.5 2.1 - - - +
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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