Contacts of the strand formed by residues 370 - 376 (chain B) in PDB entry 3NDF
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 PHE 370 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 4.4 1.8 - + - -
252A PHE* 3.6 26.5 - + - -
253A PHE 3.1 16.2 - - - +
254A LEU* 4.6 2.0 - - + -
255A PRO* 4.3 6.1 - - + -
260A LEU* 5.2 0.9 - - - -
288A LEU* 4.7 0.4 - - + -
289A PRO* 3.9 31.4 - - + -
291A LEU* 4.3 5.8 - - + -
366B PHE* 3.7 31.0 - + + -
368B LYS 3.3 20.4 - - - +
369B PRO* 1.3 74.1 - - - +
371B VAL* 1.3 75.6 - - - +
372B PHE* 3.8 15.2 - + - -
387B LYS* 3.5 5.1 - - - +
388B VAL* 3.0 60.4 + - + -
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Residues in contact with VAL 371 (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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38A TYR* 3.5 24.2 - - + +
252A PHE* 3.5 0.7 - - - -
253A PHE* 2.6 53.9 + - + +
260A LEU* 4.3 8.7 - - + -
263A LEU* 4.2 17.5 - - + +
264A GLU* 4.3 10.8 - - + -
267A LEU* 4.6 6.7 - - + -
370B PHE* 1.3 81.3 - - - +
372B PHE* 1.3 75.4 + - - +
385B MET* 4.0 26.7 - - + -
386B GLY 3.5 12.6 - - - +
387B LYS* 4.4 2.2 - - + -
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Residues in contact with PHE 372 (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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50A ILE 4.9 1.1 - - - -
51A PHE* 3.9 14.8 - + + -
250A ALA* 6.0 0.7 - - + -
251A ILE 2.9 14.6 - - - +
252A PHE* 3.6 27.6 - + + -
253A PHE* 4.0 4.9 - - - -
291A LEU* 5.7 0.9 - - + -
293A ILE* 5.5 0.9 - - + -
338A LEU* 3.4 35.9 - - + -
340A ILE* 4.9 5.6 - - + -
370B PHE* 3.8 13.2 - + - -
371B VAL* 1.3 83.3 - - - +
373B LEU* 1.3 69.1 + - - +
374B MET* 4.8 9.2 - - + -
385B MET* 3.4 12.9 - - - +
386B GLY* 3.1 53.2 + - - -
387B LYS* 4.0 1.3 - - - -
388B VAL* 3.9 22.0 - - + -
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Residues in contact with LEU 373 (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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34A ALA* 5.3 0.4 - - + -
35A PHE* 4.0 28.3 - - + -
249A THR 3.7 0.5 - - - +
250A ALA* 3.0 5.6 - - - +
251A ILE* 2.6 52.4 + - + +
253A PHE* 4.5 7.4 - - + -
267A LEU* 6.0 0.2 - - + -
272A ILE* 4.5 20.2 - - + -
372B PHE* 1.3 77.7 - - - +
374B MET* 1.3 64.4 + - - +
375B ILE* 4.0 13.6 + - + -
382B PRO* 4.1 22.7 - - + -
384B PHE 3.0 25.6 - - - +
385B MET* 3.5 24.7 - - + -
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Residues in contact with MET 374 (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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51A PHE* 4.6 2.0 - - - -
190A PHE* 3.5 46.7 - - + -
244A TYR* 3.8 12.3 - - + +
249A THR 3.5 4.3 - - - +
250A ALA* 4.3 5.8 - - + +
338A LEU* 4.2 9.2 - - - -
340A ILE* 6.1 1.1 - - + -
345A THR* 3.6 25.4 - - + -
347A ALA* 4.2 7.0 - - + -
372B PHE* 4.8 10.5 - - + -
373B LEU* 1.3 74.6 - - - +
375B ILE* 1.3 61.6 + - - +
382B PRO* 3.7 3.3 - - - +
383B LEU* 3.0 31.6 + - + +
384B PHE* 2.9 46.4 + - + +
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Residues in contact with ILE 375 (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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190A PHE* 5.6 0.2 - - - -
248A ALA* 3.2 6.6 - - - +
249A THR* 2.5 52.3 + - + +
251A ILE* 4.2 25.4 - - + -
272A ILE* 5.8 4.7 - - + -
276A LEU* 4.8 9.4 - - + -
373B LEU* 4.7 12.8 - - + -
374B MET* 1.3 74.8 - - - +
376B GLU* 1.3 76.3 + - - +
377B GLN* 4.4 2.5 - - - +
380B LYS* 3.5 31.4 - - + +
381B SER 3.4 17.7 - - - +
382B PRO* 3.8 12.6 - - + -
383B LEU* 4.4 3.8 - - - -
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Residues in contact with GLU 376 (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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102A THR* 4.3 4.5 - - - +
103A LEU* 3.7 20.0 - - + -
112A LEU* 4.4 10.3 - - + -
247A ASN* 2.6 39.2 + - - +
375B ILE* 1.3 75.5 - - - +
377B GLN* 1.3 57.9 + - - +
378B ASN* 3.0 20.0 + - - +
379B THR* 2.5 53.3 + - - +
380B LYS* 2.8 34.5 + - - -
381B SER* 3.2 13.6 + - - +
383B LEU* 3.9 16.2 - - + +
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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