Contacts of the strand formed by residues 14 - 23 (chain B) in PDB entry 2PY2
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 ARG 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B LYS 3.9 0.2 - - - +
10B MET* 3.4 6.3 - - - +
11B PHE 2.9 28.9 + - - +
12B ASN 4.2 7.9 - - - +
13B GLY* 1.3 85.3 - - - +
15B CYS* 1.3 64.9 + - - +
16B PHE* 3.7 20.7 - - + -
41B SER* 2.9 47.8 + - - +
43B HIS* 3.8 7.9 - - - -
47B GLU* 2.5 38.2 + - - -
79B ASP* 3.4 12.1 + - - -
81B THR* 5.7 2.9 - - - +
126B ALA* 3.7 18.8 - - - +
127B LYS* 3.4 14.8 - - - +
128B PRO* 4.6 6.5 - - + -
129B LEU 4.1 0.4 - - - +
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Residues in contact with CYS 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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4B CYS* 2.0 53.2 - - + -
5B PRO* 4.0 7.6 - - + -
8B TRP* 3.5 19.4 - - + -
9B LYS 3.4 5.2 - - - -
14B ARG* 1.3 74.3 - - - +
16B PHE* 1.3 62.5 + - - +
126B ALA* 3.1 6.4 - - - +
127B LYS* 2.7 37.9 + - + +
128B PRO 4.5 2.2 - - - -
129B LEU* 3.7 23.3 - - - -
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Residues in contact with PHE 16 (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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7B ASP 4.5 0.2 - - - +
8B TRP* 3.4 7.8 - - - -
9B LYS* 2.7 46.2 + - - +
11B PHE* 3.7 22.2 - + + -
14B ARG* 3.7 35.4 - - + -
15B CYS* 1.3 76.4 - - - +
17B LEU* 1.3 61.5 + - - +
40B ALA* 4.1 10.3 - - + -
41B SER 4.5 2.5 - - - -
47B GLU* 3.4 28.0 - - + -
50B PHE* 3.8 13.0 - + + -
51B VAL* 4.0 22.9 - - + -
54B LEU* 3.5 21.0 - - + +
124B ILE* 4.3 2.7 - - + -
125B CYS 3.2 7.9 - - - +
126B ALA* 3.6 22.2 - - + -
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Residues in contact with LEU 17 (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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7B ASP* 3.3 35.4 - - + +
8B TRP* 3.7 40.4 - - + +
16B PHE* 1.3 76.6 - - - +
18B PHE* 1.3 76.4 + - - +
19B ASN* 3.8 6.0 + - + +
35B GLU* 5.5 5.2 - - + -
54B LEU* 4.7 5.4 - - - -
124B ILE* 3.5 4.6 - - - +
125B CYS* 2.8 44.0 + - + +
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Residues in contact with PHE 18 (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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17B LEU* 1.3 87.1 - - - +
19B ASN* 1.3 57.8 + - - +
20B PRO* 3.4 32.0 - - + +
54B LEU* 3.4 33.1 - - + +
55B THR* 3.8 14.6 - - + -
56B SER* 6.1 0.2 - - - -
60B ILE* 3.8 28.9 - - + -
62B SER* 3.3 22.9 - - - -
122B SER* 3.6 26.0 - - - -
123B SER 3.6 5.8 - - - -
124B ILE* 3.6 20.4 - - + -
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Residues in contact with ASN 19 (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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17B LEU* 3.8 6.2 + - + -
18B PHE* 1.3 72.8 - - - +
20B PRO* 1.3 67.9 - - - +
21B LEU* 3.1 23.7 + - - +
23B LEU* 3.8 20.2 - - - +
28B ALA 5.3 0.2 + - - -
31B SER* 3.5 25.5 + - - -
122B SER* 3.3 4.0 - - - -
123B SER* 2.8 48.8 + - - +
125B CYS* 4.9 12.3 - - - -
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Residues in contact with PRO 20 (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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18B PHE* 3.4 30.5 - - + +
19B ASN* 1.3 86.5 - - - +
21B LEU* 1.3 64.9 + - - +
22B GLN* 3.5 7.1 + - - +
122B SER* 3.0 18.6 + - - +
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Residues in contact with LEU 21 (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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19B ASN* 3.1 21.4 + - - +
20B PRO* 1.3 83.3 - - + +
22B GLN* 1.3 71.5 + - + +
23B LEU* 3.4 35.5 + - + +
121B HIS 3.3 13.5 - - - +
122B SER* 3.5 4.2 - - - -
123B SER* 5.0 0.5 + - - -
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Residues in contact with GLN 22 (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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20B PRO 4.2 4.5 + - - +
21B LEU* 1.3 78.9 - - + +
23B LEU* 1.3 68.6 + - - +
60B ILE* 5.7 2.8 - - - +
61B PRO 5.6 0.4 + - - -
120B LEU* 3.4 36.0 - - + +
121B HIS* 3.7 6.7 + - - +
122B SER* 3.5 34.4 + - - +
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Residues in contact with LEU 23 (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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19B ASN* 3.8 25.6 - - - +
21B LEU* 3.9 30.3 - - + +
22B GLN* 1.3 82.0 - - - +
24B HIS* 1.3 72.4 + - - +
27B ASP* 3.8 35.2 - - + +
28B ALA* 3.9 11.2 - - + +
31B SER* 4.2 6.5 - - - +
63B TRP* 3.1 6.8 + - - -
120B LEU* 3.5 9.4 - - - -
121B HIS 2.9 27.3 + - - +
123B SER* 5.3 0.4 - - - +
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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