Contacts of the strand formed by residues 310 - 316 (chain B) in PDB entry 1LFD
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 PRO 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B GLU 3.3 25.4 - - - +
277B GLY* 3.4 2.9 - - - -
278B PHE* 3.0 23.2 + - - -
304B LYS* 6.1 0.4 - - - -
308B ASP* 3.9 7.6 - - - +
309B VAL* 1.3 81.6 - - + +
311B MET* 1.3 62.1 + - - +
359B LEU* 3.8 3.4 - - + -
362B GLU* 4.1 12.8 - - + +
363B ILE* 3.7 33.0 - - + +
366B HIS* 3.8 36.6 - - + +
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Residues in contact with MET 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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278B PHE* 3.3 21.5 - - + +
280B CYS* 4.0 16.4 - - - -
297B ARG* 3.6 43.1 - - - +
300B ILE* 4.4 16.4 - - + -
301B LYS* 4.4 6.3 - - + -
309B VAL* 3.1 39.0 + - + +
310B PRO* 1.3 78.1 - - - +
312B VAL* 1.3 70.4 + - - +
339B ILE* 3.4 39.2 - - + +
340B PRO* 3.5 5.7 - - - +
359B LEU* 3.9 2.3 - - - +
362B GLU* 4.2 6.4 - - - +
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Residues in contact with VAL 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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278B PHE 3.1 6.3 + - - -
279B LEU* 3.8 14.5 - - + -
280B CYS* 3.0 25.3 + - - -
311B MET* 1.3 81.4 - - - +
313B LEU* 1.3 69.4 + - - +
314B VAL* 3.4 15.2 + - + +
339B ILE* 4.3 1.8 - - - -
340B PRO* 3.8 24.2 - - + +
342B ILE* 4.1 23.1 - - + -
355B ALA 4.1 2.7 - - - +
358B THR* 4.2 3.6 - - + +
359B LEU* 3.7 36.8 - - + +
362B GLU* 5.0 0.9 - - + +
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Residues in contact with LEU 313 (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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280B CYS* 3.6 16.6 - - + +
282B PHE* 3.8 17.7 - - + -
293B ILE* 3.9 31.4 - - + -
312B VAL* 1.3 70.9 - - - +
314B VAL* 1.3 59.6 + - - +
330B ALA* 3.3 28.7 - - - +
333B LEU* 4.2 13.9 - - + -
334B ALA* 3.9 13.2 - - + +
337B TYR* 5.1 7.9 - - + -
339B ILE* 3.8 15.2 - - + +
340B PRO 3.0 14.4 + - - +
341B TYR* 3.3 14.5 - - + -
342B ILE 2.9 25.6 + - - -
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Residues in contact with VAL 314 (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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219B LEU* 4.0 15.3 - - + -
279B LEU* 3.6 35.2 - - + -
280B CYS 2.8 12.9 + - - +
281B VAL* 4.1 8.3 - - + -
282B PHE* 3.0 35.9 + - - +
312B VAL* 3.8 10.3 - - + +
313B LEU* 1.3 77.6 - - - +
315B GLY* 1.3 59.6 + - - +
316B ASN 4.1 2.9 - - - +
342B ILE* 3.3 4.3 - - + +
344B THR* 3.3 36.6 - - + +
355B ALA* 4.0 9.6 - - + -
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Residues in contact with GLY 315 (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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282B PHE* 3.6 25.8 - - - -
284B ILE* 4.1 7.2 - - - +
314B VAL* 1.3 68.8 - - - +
316B ASN* 1.3 60.0 + - - -
318B CYS* 4.4 1.0 - - - +
341B TYR* 3.7 14.2 - - - -
342B ILE 3.0 11.5 + - - -
343B GLU* 3.2 8.7 - - - +
344B THR 2.8 27.5 + - - +
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Residues in contact with ASN 316 (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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214B VAL 2.9 25.5 + - - +
215B GLY* 3.5 9.9 + - - -
219B LEU* 3.3 17.8 - - - +
281B VAL* 3.8 12.3 - - + -
282B PHE 2.7 16.7 + - - +
283B ALA* 3.3 1.7 - - - -
284B ILE* 3.0 21.7 + - - +
314B VAL 3.6 0.6 + - - -
315B GLY* 1.3 74.1 - - - +
317B LYS* 1.3 82.2 + - - +
318B CYS 3.4 0.9 - - - -
344B THR* 2.8 25.7 + - - +
346B ALA* 3.4 11.3 + - - +
1380B GNP 3.2 25.6 + - - -
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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