Contacts of the strand formed by residues 265 - 269 (chain B) in PDB entry 5LCM
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 MET 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B THR* 4.1 24.2 - - + -
253B GLU* 3.2 8.1 - - - +
254B LYS* 2.9 54.2 + - + +
255B PRO 4.0 7.6 - - - +
256B ASN* 4.0 4.7 - - - +
257B PRO* 3.8 35.2 - - + -
263B ALA 3.5 3.2 + - - -
264B ARG* 1.3 74.5 - - - +
266B GLN* 1.3 61.8 + - - +
267B LEU* 4.1 26.7 - - + -
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Residues in contact with GLN 266 (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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228B THR* 3.2 4.9 - - - -
229B LYS* 2.9 74.9 + - + +
243B LEU 4.9 1.2 + - - -
244B ASN* 4.5 3.8 + - - +
251B ARG* 4.1 15.7 + - - +
252B LEU 3.6 3.8 - - - -
253B GLU* 3.2 27.5 - - + +
264B ARG* 3.6 12.8 + - + +
265B MET* 1.3 80.7 - - - +
267B LEU* 1.3 62.0 + - - +
268B PHE* 3.7 20.5 - - + -
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Residues in contact with LEU 267 (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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208B PHE* 3.5 3.9 - - - -
226B LEU* 4.3 26.7 - - + +
227B LEU 3.3 5.4 - - - +
228B THR* 3.9 31.0 - - + +
251B ARG* 3.2 8.7 - - - +
252B LEU* 2.8 56.3 + - + +
254B LYS* 4.1 24.9 - - + -
265B MET* 4.1 20.2 - - + -
266B GLN* 1.3 75.6 - - - +
268B PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 268 (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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208B PHE* 4.1 7.4 - - - -
226B LEU* 3.1 4.7 - - - -
227B LEU* 2.7 42.7 + - - +
229B LYS* 3.9 14.1 - - + -
232B CYS* 3.8 11.7 - - - -
243B LEU* 3.7 47.1 - - + -
249B PHE* 3.8 22.2 - + + -
250B HIS 3.8 12.6 - - - +
251B ARG* 4.0 21.8 - - + -
266B GLN* 3.7 30.5 - - + -
267B LEU* 1.3 76.5 - - - +
269B VAL* 1.3 61.9 + - - +
272B GLU* 6.4 0.2 - - + -
273B VAL* 3.5 19.5 - - + -
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Residues in contact with VAL 269 (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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204B LEU* 3.9 17.5 - - + -
208B PHE* 3.5 34.4 - - + -
210B LEU* 4.6 2.7 - - + -
223B LYS 3.8 11.9 - - - +
224B TYR* 3.6 24.0 - - - +
225B ALA 3.6 1.8 - - - -
226B LEU* 4.0 4.9 - - + -
250B HIS 4.9 0.4 + - - -
268B PHE* 1.3 74.6 - - - +
270B ARG* 1.3 68.9 + - - +
271B CYS* 3.9 13.7 - - - -
272B GLU* 3.1 33.0 + - + +
273B VAL* 3.2 13.1 + - - +
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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