Contacts of the strand formed by residues 9 - 15 (chain B) in PDB entry 1PL8
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 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN* 3.1 15.7 + - - +
8B ASN* 1.3 74.3 - - - +
10B SER* 1.3 59.7 + - - +
21B LEU* 4.1 30.5 - - + +
22B GLU* 3.5 27.4 - - - +
23B ASN* 3.7 8.2 + - + +
129B CYS* 3.1 21.5 - - - -
130B ARG* 3.3 28.2 + - - +
327B LEU* 3.6 13.0 - - + +
328B GLU* 4.1 18.6 - - + -
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Residues in contact with SER 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN* 2.8 17.5 + - - -
9B LEU* 1.3 74.1 - - - +
11B LEU* 1.3 61.5 + - - +
12B VAL* 3.6 5.4 + - - +
20B ARG 3.4 0.7 - - - +
21B LEU* 3.3 9.4 - - - -
22B GLU 2.7 36.0 + - - +
24B TYR* 3.7 23.5 - - - +
66B VAL* 4.1 14.4 - - - +
128B LEU 3.5 6.3 - - - -
129B CYS* 3.3 17.0 - - - +
327B LEU* 5.1 0.4 - - - -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER* 1.3 71.1 - - - +
12B VAL* 1.3 59.4 + - - +
19B LEU* 3.6 32.8 - - + -
20B ARG 3.5 9.4 - - - +
21B LEU* 3.9 15.7 - - + +
66B VAL* 3.3 6.6 - - - +
67B LEU* 3.0 27.9 + - + -
128B LEU* 3.0 38.0 + - + +
327B LEU* 4.5 5.1 - - + +
330B ALA* 3.6 24.7 - - + -
331B LEU 5.2 0.4 - - - +
334B PHE* 3.3 38.8 - - + -
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER 3.8 6.1 - - - +
11B LEU* 1.3 80.3 - - - +
13B VAL* 1.3 65.2 + - - +
14B HIS* 3.8 4.6 + - + -
18B ASP 3.7 0.5 - - - +
19B LEU* 3.4 4.9 - - - +
20B ARG 2.7 40.3 + - - +
22B GLU* 3.0 35.4 - - + +
24B TYR* 3.6 31.2 - - + +
64B PRO* 3.7 15.9 - - + -
65B MET 3.4 25.8 - - - +
66B VAL* 4.1 5.8 - - + -
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 1.3 70.6 - - - +
14B HIS* 1.3 63.9 + - - +
15B GLY* 3.7 19.7 - - - +
18B ASP 3.5 4.3 - - - +
19B LEU* 3.7 10.3 - - + -
50B TYR 3.4 22.9 - - - +
51B TRP* 4.0 13.9 - - - +
54B GLY* 4.9 0.2 - - - -
61B VAL* 3.8 17.8 - - + +
64B PRO* 3.3 2.4 - - - +
65B MET* 2.8 37.0 + - + +
67B LEU* 3.3 44.2 - - + -
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Residues in contact with HIS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.8 11.5 - - + +
13B VAL* 1.3 74.6 - - - +
15B GLY* 1.3 58.1 + - - +
18B ASP* 2.9 27.3 + - - +
20B ARG* 3.5 45.2 + - + +
22B GLU* 2.4 39.2 + - - -
61B VAL* 4.8 9.3 - - - +
63B LYS 5.4 0.7 - - - -
64B PRO* 3.3 34.9 - - + +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.5 13.6 - - - +
14B HIS* 1.3 79.0 - - - +
16B PRO* 1.3 78.8 - - - +
17B GLY 3.2 1.0 + - - -
18B ASP* 2.9 17.5 + - - +
51B TRP 3.5 5.5 - - - +
54B GLY* 4.5 5.4 - - - -
61B VAL* 5.5 4.5 - - - -
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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