Contacts of the strand formed by residues 519 - 526 (chain A) in PDB entry 2PMF
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 ASN 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A PHE* 3.5 3.3 - - - -
301A VAL* 2.8 39.7 + - + +
303A PRO* 3.8 30.4 - - + +
306A LYS* 3.8 28.1 - - - +
409A ASP* 4.9 3.0 + - - +
410A ARG 3.6 11.9 - - - +
411A SER* 3.5 30.8 + - - +
517A VAL 3.6 2.7 + - - +
518A PRO* 1.3 74.1 - - - +
520A VAL* 1.3 59.1 + - - +
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Residues in contact with VAL 520 (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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251A PHE* 4.6 3.8 - - + -
298A GLU* 3.0 29.2 - - - +
299A HIS 3.2 16.2 - - - +
300A PHE* 4.0 24.0 - - + -
408A ALA 3.4 3.5 - - - +
410A ARG* 3.1 39.3 + - + +
413A TYR* 3.8 33.2 - - + -
518A PRO 4.7 1.3 - - - +
519A ASN* 1.3 74.7 - - - +
521A ILE* 1.3 68.6 + - - +
522A GLU* 4.7 4.6 - - + +
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Residues in contact with ILE 521 (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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299A HIS* 2.9 41.2 + - + +
301A VAL* 3.9 6.5 - - + -
306A LYS* 3.0 34.1 - - - +
351A VAL* 3.8 19.3 - - + -
352A LEU* 4.5 11.7 - - + -
355A PHE* 3.8 25.4 - - + -
407A CYS* 4.1 17.3 - - - -
408A ALA 3.3 6.3 - - - +
409A ASP* 3.6 21.8 - - + +
520A VAL* 1.3 74.3 - - - +
522A GLU* 1.3 61.8 + - - +
523A PRO* 3.4 12.8 - - + +
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Residues in contact with GLU 522 (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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247A ALA* 4.0 6.6 - - - +
251A PHE* 4.0 6.6 - - - -
296A GLU* 4.5 11.1 - - - +
297A ILE 3.0 6.3 - - - +
298A GLU* 2.9 41.7 - - - +
406A GLY 3.4 8.1 - - - +
407A CYS* 4.3 0.4 - - - -
408A ALA* 3.0 29.2 + - + +
410A ARG* 3.1 42.4 + - - +
520A VAL* 4.7 4.0 - - + +
521A ILE* 1.3 74.4 - - - +
523A PRO* 1.3 64.3 - - - +
524A SER* 3.5 7.4 + - - -
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Residues in contact with PRO 523 (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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296A GLU* 3.8 0.7 - - - -
297A ILE* 3.0 60.9 + - + +
355A PHE* 4.3 16.6 - - + -
359A ILE* 3.8 27.1 - - + -
406A GLY 3.1 7.6 - - - +
407A CYS* 4.1 6.0 - - - -
521A ILE* 3.4 18.2 - - + +
522A GLU* 1.3 83.7 - - - +
524A SER* 1.3 59.7 + - - +
525A PHE* 3.8 15.3 - - + -
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Residues in contact with SER 524 (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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294A MET* 4.9 6.7 - - - -
295A ALA 3.5 3.8 - - - -
296A GLU* 3.4 31.4 - - - -
403A GLU* 4.6 1.7 + - - +
405A VAL* 3.3 4.4 - - - -
406A GLY* 2.6 46.3 + - - -
522A GLU* 3.5 8.9 + - - -
523A PRO* 1.3 72.4 - - - +
525A PHE* 1.3 62.7 + - - +
526A ARG* 3.9 2.4 + - - +
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Residues in contact with PHE 525 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A TRP* 3.3 41.3 - + - +
115A PHE* 3.4 28.5 - + - -
294A MET* 3.1 22.0 - - - +
295A ALA* 2.7 38.1 + - + +
297A ILE* 4.3 3.4 - - + -
359A ILE* 3.8 19.7 - - + -
362A TYR* 4.2 9.6 - + - -
404A ILE 4.0 2.2 - - - -
405A VAL* 3.6 25.4 - - + -
523A PRO* 3.8 23.1 - - + -
524A SER* 1.3 76.0 - - - +
526A ARG* 1.3 59.1 + - - +
527A LEU* 3.2 8.5 + - + -
530A ILE* 4.0 15.0 - - + -
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Residues in contact with ARG 526 (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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277A ARG* 3.6 26.5 - - - +
287A ILE 3.7 6.7 + - - -
289A VAL* 4.1 7.3 + - - +
292A PHE* 3.7 40.1 - - - -
293A THR 4.7 0.9 - - - -
294A MET* 4.2 13.2 - - - -
403A GLU* 4.2 23.2 + - - +
404A ILE 2.8 21.5 + - - +
524A SER 3.9 1.5 + - - +
525A PHE* 1.3 68.7 - - - +
527A LEU* 1.3 60.4 + - - +
528A GLY 3.3 2.7 - - - -
529A ARG* 3.1 54.0 + - - +
530A ILE* 2.9 29.9 + - - +
901A CL 3.2 21.8 - - + +
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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