Contacts of the helix formed by residues 303 - 312 (chain B) in PDB entry 2HW6
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 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 3.1 37.3 + - - -
301B HIS 3.9 3.0 + - - -
302B ILE* 1.3 77.8 - - - +
304B SER* 1.3 72.0 + - - +
305B GLU* 2.9 24.4 + - - +
306B ALA* 3.6 8.4 + - - +
307B LYS* 3.3 21.5 + - - +
332B TRP* 4.6 0.9 + - - -
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Residues in contact with SER 304 (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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303B SER* 1.3 74.5 + - - +
305B GLU* 1.3 71.7 + - - -
306B ALA 3.0 3.8 - - - -
307B LYS* 2.9 5.7 + - - +
308B ASP* 2.6 38.0 + - - +
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Residues in contact with GLU 305 (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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303B SER* 2.9 21.8 + - - -
304B SER* 1.3 87.1 + - - +
306B ALA* 1.3 62.3 + - - +
308B ASP* 3.8 10.1 - - - +
309B LEU* 3.4 4.5 + - - +
330B HIS* 3.3 31.3 - - + -
331B PRO* 5.0 11.7 - - + -
332B TRP* 3.6 24.9 - - + +
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Residues in contact with ALA 306 (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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144B GLU* 3.4 25.4 - - - +
250B LEU* 4.7 1.6 - - - +
254B LEU* 4.4 10.5 - - + -
302B ILE* 6.0 1.1 - - + -
303B SER* 3.6 15.0 + - - +
304B SER 3.0 0.2 + - - -
305B GLU* 1.3 80.5 - - - +
307B LYS* 1.3 59.9 + - - +
308B ASP 3.0 5.2 + - - -
309B LEU* 3.2 11.4 + - - +
310B ILE* 3.4 16.0 + - - +
332B TRP* 3.5 29.9 - - + +
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Residues in contact with LYS 307 (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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251B TYR* 4.9 8.0 - - - -
254B LEU* 6.4 1.1 - - + -
299B TRP* 3.3 52.5 - - + +
302B ILE* 4.7 16.6 - - + -
303B SER 3.3 11.1 + - - +
304B SER* 2.9 7.6 + - - +
306B ALA* 1.3 75.0 - - + +
308B ASP* 1.3 59.3 + - - +
310B ILE* 4.0 23.8 - - + -
311B SER* 3.0 22.6 + - - -
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Residues in contact with ASP 308 (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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304B SER 2.6 20.6 + - - +
305B GLU* 3.8 11.6 - - - +
306B ALA 3.0 0.2 + - - -
307B LYS* 1.3 71.3 - - - +
309B LEU* 1.3 65.7 + - - +
310B ILE 3.0 1.3 - - - -
311B SER* 3.0 12.4 + - - -
312B LYS* 3.0 48.1 + - - +
330B HIS* 3.1 19.1 + - - -
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Residues in contact with LEU 309 (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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151B VAL* 4.2 11.2 - - + -
250B LEU* 3.9 16.4 - - + -
305B GLU 3.4 6.3 + - - +
306B ALA 3.2 10.1 + - - +
308B ASP* 1.3 77.0 - - - +
310B ILE* 1.3 61.0 + - - +
312B LYS* 3.5 3.4 + - - +
313B LEU* 3.2 40.0 + - + +
322B LEU* 3.8 19.5 - - + -
327B VAL* 4.4 10.8 - - + -
330B HIS* 3.6 38.3 + - + +
332B TRP* 3.8 26.0 - - + -
333B VAL* 4.2 17.7 - - + -
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Residues in contact with ILE 310 (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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247B GLY* 4.4 7.0 - - - +
250B LEU* 3.7 29.4 - - + -
251B TYR* 3.9 40.6 - - + +
254B LEU* 4.1 20.0 - - + -
299B TRP* 5.9 0.4 - - + -
306B ALA 3.4 9.5 + - - +
307B LYS* 4.1 24.7 - - + +
308B ASP 3.0 1.2 - - - -
309B LEU* 1.3 75.3 - - - +
311B SER* 1.3 61.7 + - - +
313B LEU* 3.0 8.5 + - - +
314B LEU* 2.8 49.5 + - + +
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LYS* 3.0 20.6 + - - -
308B ASP* 3.0 16.5 + - - -
310B ILE* 1.3 79.6 - - - +
312B LYS* 1.3 59.5 + - - +
313B LEU 3.2 1.6 + - - -
314B LEU* 4.1 5.1 - - - +
315B VAL* 3.4 26.7 + - - +
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Residues in contact with LYS 312 (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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308B ASP* 3.0 42.7 + - - +
309B LEU 3.7 4.3 - - - +
310B ILE 3.2 0.2 - - - -
311B SER* 1.3 76.5 - - - +
313B LEU* 1.3 58.4 + - - +
315B VAL* 3.7 5.9 - - - +
320B GLN 4.8 0.3 - - - +
321B ARG* 3.7 8.7 - - - -
322B LEU* 3.6 59.8 + - + +
330B HIS* 4.5 10.5 - - + -
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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