Contacts of the strand formed by residues 11 - 20 (chain E) in PDB entry 2WFK
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 LYS 11 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E PRO* 5.5 2.6 - - - +
9E SER* 3.2 37.6 + - - +
10E LEU* 1.3 78.1 - - - +
12E SER* 1.3 66.9 + - - +
31E PHE* 4.0 36.3 - - + +
32E LEU 4.3 4.0 - - - +
33E PRO* 4.6 14.1 - - + -
34E TYR* 3.3 10.1 - - - -
150E THR* 5.7 6.9 - - - +
164E ARG* 2.9 30.3 + - - +
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Residues in contact with SER 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LYS* 1.3 79.2 - - - +
13E SER* 1.3 58.5 + - - +
14E PHE* 3.0 23.6 + - - +
31E PHE* 3.3 20.8 - - - +
32E LEU* 2.4 29.0 + - - +
34E TYR* 3.3 35.4 - - - +
73E GLU* 3.6 6.7 - - - -
164E ARG* 4.1 2.3 + - - -
214E LEU* 4.3 12.5 - - - +
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Residues in contact with SER 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E SER* 1.3 71.2 - - - +
14E PHE* 1.3 61.0 + - - +
15E VAL* 3.5 7.3 + - - +
31E PHE* 3.8 16.3 - - - -
73E GLU* 2.8 27.9 + - - -
164E ARG* 3.8 20.8 - - - +
166E LYS* 3.0 31.6 + - - +
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Residues in contact with PHE 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PRO 5.2 3.1 - - - -
69D ALA* 6.1 3.4 - - + -
188D ARG* 4.3 25.1 - - - -
241D GLU* 5.1 6.1 - - - -
12E SER* 3.0 18.5 + - - +
13E SER* 1.3 77.4 + - - +
15E VAL* 1.3 74.2 + - - +
16E LEU* 4.3 12.6 - - + -
31E PHE* 3.5 2.9 - - - -
32E LEU* 2.9 48.5 + - + -
73E GLU* 5.3 1.3 - - - +
169E ASN* 3.8 32.1 - - - -
214E LEU* 4.7 14.1 - - + -
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Residues in contact with VAL 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E SER 3.5 5.5 + - - +
14E PHE* 1.3 84.3 - - - +
16E LEU* 1.3 60.1 + - - +
17E SER 3.3 28.9 - - - +
18E GLU* 4.0 17.5 - - + +
29E LYS* 4.1 22.7 - - + +
30E THR 3.8 5.6 - - - +
31E PHE* 3.5 25.4 - - + -
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D LEU* 4.1 29.4 - - + +
245D LYS* 4.3 29.8 - - + +
248D ALA* 3.3 33.2 - - + -
14E PHE* 3.4 14.8 + - + -
15E VAL* 1.3 74.9 - - - +
17E SER* 1.3 59.5 + - - +
30E THR* 2.8 19.3 + - + +
31E PHE 4.1 5.2 - - - +
32E LEU* 3.8 45.1 - - + +
33E PRO* 4.9 0.4 - - + -
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Residues in contact with SER 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D LYS* 5.1 12.8 - - - +
15E VAL* 3.3 10.1 - - - +
16E LEU* 1.3 80.9 - - - +
18E GLU* 1.3 70.7 + - - +
19E SER* 5.3 2.8 + - - -
28E VAL* 4.1 3.7 + - - +
29E LYS* 3.4 1.6 - - - -
30E THR* 3.0 44.8 + - - -
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Residues in contact with GLU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 4.0 10.5 - - + +
17E SER* 1.3 79.6 + - - +
19E SER* 1.3 66.6 + - - +
27E THR* 3.9 15.9 + - - +
28E VAL 3.0 9.2 - - - +
29E LYS* 3.1 38.9 + - + +
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E SER* 5.3 2.9 - - - -
18E GLU* 1.3 78.7 - - - +
20E THR* 1.3 70.1 + - - +
27E THR* 3.0 9.9 - - - -
28E VAL* 2.8 45.2 + - - +
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Residues in contact with THR 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E SER* 1.3 85.9 + - - +
21E VAL* 1.3 96.1 + - - +
22E PRO* 3.4 17.7 - - + +
24E THR 5.8 0.7 - - - +
26E GLU 4.2 8.3 - - - +
27E THR* 4.3 7.0 - - + +
28E VAL 5.2 0.2 - - - -
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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