Contacts of the helix formed by residues 304 - 312 (chain B) in PDB entry 3LXC
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 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271B GLY* 5.5 1.9 + - - -
303B ILE* 1.3 78.2 - - - +
305B PRO* 1.3 74.2 - - - +
306B GLN* 3.7 7.5 + - - +
307B ALA* 3.1 26.0 + - - +
308B LYS* 3.0 21.4 + - - +
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Residues in contact with PRO 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 ILE 3.7 3.1 - - - +
304B SER* 1.3 87.6 - - - +
306B GLN* 1.3 56.4 + - - +
308B LYS* 3.4 11.6 + - + +
309B ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 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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277B TRP* 3.4 64.7 - - + +
304B SER* 3.1 7.3 - - - +
305B PRO* 1.3 80.4 - - - +
307B ALA* 1.3 61.3 + - - +
309B ALA* 3.5 6.9 + - + +
310B LEU 3.2 16.8 + - - -
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Residues in contact with ALA 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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270B ILE* 4.2 12.6 - - + -
271B GLY* 3.9 27.6 - - - -
277B TRP* 4.3 7.1 - - + -
280B GLN* 4.6 3.8 - - - +
303B ILE* 3.9 9.9 - - + -
304B SER* 3.1 23.7 + - - +
306B GLN* 1.3 74.4 - - - +
308B LYS* 1.3 58.9 + - - +
310B LEU* 3.3 3.0 + - - +
311B LEU* 3.0 36.5 + - - +
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Residues in contact with LYS 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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79B GLU* 3.1 53.4 + - + +
81B TRP* 3.7 21.5 - - + -
303B ILE* 4.5 10.9 - - + +
304B SER 3.0 16.6 + - - +
305B PRO* 3.6 9.6 - - + +
307B ALA* 1.3 76.6 - - - +
309B ALA* 1.3 58.4 + - - +
311B LEU 3.5 0.5 + - - -
312B GLN* 3.0 57.7 + - - +
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Residues in contact with ALA 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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305B PRO 2.9 17.7 + - - +
306B GLN* 3.8 8.5 - - + +
307B ALA 3.3 0.2 - - - -
308B LYS* 1.3 76.8 - - - +
310B LEU* 1.3 62.1 - - - +
312B GLN* 3.6 3.5 + - - -
313B ASP* 3.1 24.8 + - - +
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Residues in contact with LEU 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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270B ILE* 3.8 20.9 - - + -
277B TRP* 3.9 18.4 - - + -
280B GLN* 3.5 35.2 - - + +
281B VAL* 3.9 10.3 - - + +
284B MET* 3.6 25.5 - - + +
306B GLN 3.2 12.6 + - - +
307B ALA 3.6 7.2 - - - +
308B LYS 3.3 0.2 - - - -
309B ALA* 1.3 80.2 - - - +
311B LEU* 1.3 63.6 + - - +
313B ASP* 3.1 22.9 + - + +
388B LEU* 3.6 32.3 - - + -
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Residues in contact with LEU 311 (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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81B TRP* 3.6 27.1 - - + -
86B TYR* 2.8 31.7 + - - +
268B LEU* 3.7 31.0 - - + -
270B ILE* 3.8 39.3 - - + +
284B MET* 3.6 6.8 - - - +
296B MET* 4.0 9.9 - - + -
298B ASN* 3.9 24.2 - - - +
303B ILE* 4.1 6.3 - - + -
307B ALA 3.0 20.2 + - - +
310B LEU* 1.3 76.6 - - - +
312B GLN* 1.3 58.8 + - - +
313B ASP 3.4 0.2 - - - -
317B ILE* 3.5 8.0 - - - +
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Residues in contact with GLN 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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79B GLU 3.0 24.4 + - - +
80B GLY* 4.2 10.8 - - - +
81B TRP* 3.2 49.7 - - + +
84B ALA* 4.0 14.6 - - + +
308B LYS* 3.0 33.9 + - - +
309B ALA* 3.7 4.2 - - - +
311B LEU* 1.3 75.7 - - - +
313B ASP* 1.3 64.2 + - - +
314B LYS* 2.9 8.3 + - - +
317B ILE* 3.8 11.4 - - - +
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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