Contacts of the strand formed by residues 401 - 405 (chain A) in PDB entry 2FGY
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 TYR 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.6 36.6 - + - -
131A THR* 5.1 2.9 - - + -
135A LEU* 3.5 14.2 - - + +
400A ARG* 1.3 79.8 - - + +
402A ILE* 1.3 73.2 + - - +
403A SER* 4.0 12.8 - - - -
408A PHE* 4.3 7.8 - + - -
411A VAL* 3.4 28.9 + - - +
416A LEU* 3.4 25.6 + - + +
417A ALA* 3.2 23.9 - - + +
418A TYR 3.1 22.5 + - - -
439A PHE* 3.4 12.7 - - - -
451A PRO* 3.6 24.0 - - + +
453A ALA* 4.2 16.8 - - + +
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Residues in contact with ILE 402 (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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401A TYR* 1.3 75.8 - - - +
403A SER* 1.3 58.2 + - - +
404A VAL* 3.6 25.4 - - + -
418A TYR* 3.4 20.9 - - + +
432A VAL* 5.3 4.9 - - + +
435A GLY* 3.7 32.1 - - - +
436A ILE* 3.9 14.6 - - + -
439A PHE* 3.5 21.1 - - + -
450A ILE* 3.6 26.0 - - + -
451A PRO 3.1 7.7 + - - +
452A ILE* 3.5 12.5 - - + -
453A ALA 2.8 26.3 + - - +
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Residues in contact with SER 403 (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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179A LYS* 5.9 1.1 - - - -
401A TYR* 4.0 20.8 - - - -
402A ILE* 1.3 72.8 - - - +
404A VAL* 1.3 64.7 + - - +
407A GLY* 4.1 8.3 + - - -
408A PHE* 3.8 22.5 + - - -
417A ALA* 4.4 4.0 - - - -
418A TYR 2.7 14.3 + - - +
419A TYR* 3.3 20.5 - - - -
420A ALA 2.9 25.8 + - - -
453A ALA 3.4 5.0 + - - -
455A HIS* 5.4 0.9 - - - +
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Residues in contact with VAL 404 (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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402A ILE* 3.6 21.1 - - + -
403A SER* 1.3 81.8 + - - +
405A GLY* 1.3 60.3 + - - +
406A ASP 4.2 0.2 + - - -
407A GLY 5.1 0.2 - - - -
419A TYR* 4.8 0.4 - - - -
420A ALA* 3.3 13.0 - - + +
422A LEU* 4.2 20.0 - - + -
432A VAL* 4.9 8.1 - - + -
452A ILE* 4.3 5.2 - - + -
453A ALA 2.9 9.3 + - - +
454A ILE* 3.5 30.1 - - + +
455A HIS* 3.1 25.5 + - - +
456A TYR* 4.9 0.4 - - - -
476A ILE* 3.9 17.0 - - + -
480A ILE* 4.3 11.7 - - + -
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Residues in contact with GLY 405 (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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404A VAL* 1.3 75.3 - - - +
406A ASP* 1.3 65.3 + - - -
407A GLY 3.4 0.9 - - - -
419A TYR* 3.1 13.6 + - - -
420A ALA 3.1 8.9 + - - -
421A HIS* 3.2 19.5 - - - -
422A LEU* 3.6 8.3 + - - +
455A HIS 3.4 2.2 - - - -
456A TYR* 3.4 27.8 - - - -
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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