Contacts of the helix formed by residues 20 - 29 (chain B) in PDB entry 6WCZ
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 SER 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A GLU* 2.7 23.9 + - - -
16B LEU 5.0 0.5 - - - +
19B MET* 1.3 82.1 - - - +
21B ALA* 1.3 69.6 + - - +
22B LEU* 4.1 1.5 + - - -
23B GLU* 2.8 30.0 + - - +
24B PHE* 3.8 6.2 + - - +
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Residues in contact with ALA 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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299A LEU* 5.5 10.8 - - + -
302A ALA* 5.1 7.4 - - + -
303A GLN* 4.5 22.9 - - + +
306A GLU* 3.3 15.0 - - - +
20B SER* 1.3 80.4 + - - +
22B LEU* 1.3 59.0 + - - +
23B GLU 3.1 1.6 - - - -
24B PHE* 3.0 9.6 + - - +
25B TYR* 2.9 29.3 + - - +
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Residues in contact with LEU 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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225A THR* 4.6 12.6 - - + +
303A GLN* 3.8 27.1 - - + +
306A GLU* 2.6 38.2 + - + +
307A LEU* 5.1 15.3 - - + -
310A ARG* 4.0 25.4 - - + +
20B SER* 4.1 0.8 + - - +
21B ALA* 1.3 72.7 - - - +
23B GLU* 1.3 51.5 + - - +
25B TYR* 4.3 10.3 - - + +
26B SER* 2.3 47.1 + - - -
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Residues in contact with GLU 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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16B LEU* 3.4 33.1 - - - +
19B MET* 3.2 29.7 - - + +
20B SER* 2.8 39.8 - - - +
22B LEU* 1.3 76.5 - - - +
24B PHE* 1.3 71.4 + - - +
26B SER* 3.3 6.0 + - - -
27B TYR* 2.9 31.9 + - - +
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Residues in contact with PHE 24 (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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299A LEU* 5.4 21.1 - - + -
16B LEU* 5.0 19.7 - - + +
20B SER 3.9 10.3 - - - +
21B ALA* 3.0 10.6 + - - +
23B GLU* 1.3 89.2 - - - +
25B TYR* 1.3 65.8 + + + +
27B TYR* 3.5 3.2 + + - +
28B LYS* 2.9 45.5 + - + +
215B SER* 3.2 35.9 - - - -
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Residues in contact with TYR 25 (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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218A LYS* 4.7 21.3 + - - -
221A LEU* 5.5 2.6 - - + +
222A GLY* 3.9 21.6 + - - -
225A THR* 4.7 15.9 - - + -
303A GLN* 3.2 37.7 - - - +
21B ALA 2.9 14.8 + - - +
22B LEU* 4.4 9.0 - - + -
24B PHE* 1.3 82.9 - + + +
26B SER* 1.3 63.4 + - - +
28B LYS* 3.4 21.2 + - + +
29B LYS* 3.8 22.5 + - + +
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Residues in contact with SER 26 (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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22B LEU* 2.3 32.9 + - - -
23B GLU* 3.3 9.7 + - - -
25B TYR* 1.3 78.5 - - - +
27B TYR* 1.3 66.0 + - - +
29B LYS* 4.2 1.6 + - - +
30B SER* 3.3 19.4 + - - -
248B ARG* 4.4 28.8 + - - +
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Residues in contact with TYR 27 (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 TRP* 3.2 29.5 - + - -
16B LEU* 4.5 22.2 - - + -
23B GLU* 2.9 22.8 + - - +
24B PHE* 3.9 3.1 - + - +
26B SER* 1.3 79.5 + - - +
28B LYS* 1.3 53.2 + - - +
30B SER* 2.8 17.5 + - - -
214B ASN* 2.4 65.1 + - + -
215B SER* 4.5 4.9 - - - -
243B ARG 2.7 27.9 + - - -
244B MET 3.2 24.1 + - - -
245B ASP* 4.2 12.6 - - - +
248B ARG* 6.1 0.9 - - - -
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Residues in contact with LYS 28 (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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24B PHE* 2.9 31.6 + - + +
25B TYR* 3.8 13.5 - - + +
26B SER 3.4 0.6 - - - -
27B TYR* 1.3 77.9 - - - +
29B LYS* 1.3 67.8 + - + +
32B ILE* 4.0 3.8 - - - +
213B ARG* 3.0 58.5 - - - +
214B ASN* 3.2 28.9 + - - +
215B SER* 3.7 23.6 + - - +
216B THR* 5.7 1.2 + - - -
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Residues in contact with LYS 29 (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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25B TYR* 3.8 26.2 + - + +
26B SER 4.2 2.2 + - - +
27B TYR 3.2 0.2 - - - -
28B LYS* 1.3 92.6 - - + +
30B SER* 1.3 59.6 + - - +
31B GLY 3.5 0.2 + - - -
32B ILE* 3.3 20.0 - - + +
34B GLU* 2.7 33.4 + - - +
37B ARG* 4.2 17.2 - - - +
213B ARG* 4.6 11.3 - - - +
214B ASN* 3.6 2.0 - - - -
251B VAL* 3.4 23.1 - - + +
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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