Contacts of the strand formed by residues 245 - 249 (chain A) in PDB entry 1LAN
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 LEU 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A PRO 4.9 1.3 - - - +
244A PRO* 1.3 75.3 - - + +
246A VAL* 1.3 59.8 + - - +
247A PHE* 4.5 9.0 - - + -
294A ILE* 4.4 14.8 - - + -
295A ASN 3.0 18.3 + - - +
296A ILE* 3.4 9.8 - - + +
297A VAL 2.9 23.6 + - - -
352A LYS* 4.6 10.3 - - + -
353A VAL* 4.0 28.7 - - + +
478A PHE* 4.0 8.1 - - + -
479A LEU* 3.9 23.3 - - + -
482A PHE* 3.6 50.0 - - + -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PRO* 4.4 2.9 - - + -
245A LEU* 1.3 76.1 - - - +
247A PHE* 1.3 79.2 + - - +
248A VAL* 4.2 2.9 - - + -
297A VAL* 3.4 20.4 - - + +
299A LEU* 4.0 13.5 - - + -
346A ALA* 3.9 26.0 - - + +
349A PHE* 4.1 17.9 - - + -
351A PRO* 3.4 25.4 - - + -
353A VAL* 3.1 13.8 + - - +
354A ILE* 3.5 6.0 - - + -
355A ILE 2.9 24.9 + - - -
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Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.5 10.3 - - + -
246A VAL* 1.3 83.3 - - - +
248A VAL* 1.3 58.9 + - - +
280A ILE* 3.8 41.3 - - + -
283A ALA* 4.9 1.8 - - + -
284A ILE* 4.3 10.1 - - + -
296A ILE* 4.3 13.2 - - + -
297A VAL 2.8 10.5 + - - +
298A GLY* 3.3 1.0 - - - -
299A LEU 2.8 31.2 + - - -
353A VAL* 5.3 0.7 - - + -
355A ILE* 3.1 35.0 - - + +
475A LEU* 4.1 29.6 - - + -
478A PHE* 4.3 6.3 - + - -
479A LEU* 3.8 39.3 - - + -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 4.2 14.8 - - + -
247A PHE* 1.3 79.4 - - - +
249A GLY* 1.3 63.0 + - - +
280A ILE* 4.1 7.3 - - - +
299A LEU* 3.2 15.7 - - + +
301A PRO* 4.7 0.2 - - + -
339A LEU* 3.9 17.7 - - + -
342A ALA* 3.5 31.6 - - + +
343A LEU* 4.3 14.4 - - + +
346A ALA* 4.2 15.3 - - + -
354A ILE* 4.5 5.6 - - + -
355A ILE 2.8 9.1 + - - +
356A ASN* 3.0 15.9 - - + +
357A ALA 2.9 25.1 + - - -
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Residues in contact with GLY 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL* 1.3 75.7 - - - +
250A LYS* 1.3 64.9 + - - -
251A GLY 3.3 3.6 + - - -
276A GLY 3.8 16.6 - - - -
277A ALA* 3.8 7.6 - - - -
280A ILE* 3.9 3.1 - - - +
299A LEU 2.9 12.3 + - - -
300A ALA* 3.5 7.6 - - - +
301A PRO* 3.4 18.5 - - - +
339A LEU* 4.3 5.2 - - - -
357A ALA 3.5 6.1 - - - -
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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