Contacts of the strand formed by residues 595 - 602 (chain A) in PDB entry 2P4E
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 SER 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A THR* 5.0 1.6 - - - -
539A ALA 3.2 11.9 - - - -
540A PRO* 3.6 6.1 - - - +
541A PRO* 3.4 19.1 - - - +
564A SER* 2.7 30.1 + - - -
565A HIS* 2.8 40.1 + - - -
566A TRP* 4.9 0.4 - - - +
567A GLU* 5.2 2.6 + - - -
594A ALA* 1.3 72.8 - - - +
596A ILE* 1.3 60.0 + - - +
597A HIS* 3.9 8.7 - - - -
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Residues in contact with ILE 596 (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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537A HIS 3.7 1.0 - - - +
538A THR* 3.3 4.2 - - - -
539A ALA* 2.8 41.1 + - + +
548A THR* 3.3 35.2 - - + +
549A ARG 3.8 0.9 - - - +
550A VAL* 3.7 20.4 - - + -
562A CYS* 5.5 0.7 - - + -
563A SER 3.7 9.2 - - - +
564A SER* 5.1 1.3 - - - +
588A CYS* 3.0 50.0 - - + +
589A VAL* 3.2 21.3 - - - +
590A GLY* 3.4 4.3 - - - +
595A SER* 1.3 73.9 - - - +
597A HIS* 1.3 67.8 + - - +
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Residues in contact with HIS 597 (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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498A GLU 3.7 12.8 - - - -
499A ARG* 3.4 28.8 - - + +
500A MET* 3.6 21.2 + - + +
536A VAL* 4.1 5.8 - - + -
537A HIS 3.4 3.4 - - - -
538A THR* 2.7 41.3 + - + +
550A VAL* 4.4 1.6 - - - -
562A CYS* 3.4 4.7 - - - -
563A SER* 2.8 44.6 + - - +
564A SER* 4.0 2.9 - - - -
565A HIS* 2.9 37.1 + + - -
588A CYS* 4.2 1.4 - - - -
595A SER* 3.9 7.9 - - - -
596A ILE* 1.3 76.4 - - - +
598A ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 598 (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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500A MET* 4.0 2.9 - - - -
536A VAL* 3.2 5.9 - - - -
537A HIS* 2.8 37.0 + - + +
550A VAL* 3.8 19.7 - - + +
551A HIS* 5.3 1.3 - - - -
552A CYS* 4.6 1.3 - - - -
559A LEU* 3.7 10.8 - - + -
561A GLY 3.6 3.8 - - - -
588A CYS* 3.6 20.0 - - - -
597A HIS* 1.3 74.3 - - - +
599A SER* 1.3 60.8 + - - +
600A CYS* 3.6 11.9 + - - -
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Residues in contact with SER 599 (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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483A LEU 4.0 4.7 + - - -
484A LEU* 3.2 25.9 + - - -
500A MET* 3.6 22.6 - - - +
534A CYS* 5.1 1.4 - - - +
535A SER 3.5 6.4 + - - -
536A VAL* 4.7 2.9 - - - +
559A LEU* 3.4 7.3 - - - +
560A THR* 2.7 46.7 + - - -
561A GLY 2.9 11.7 + - - -
598A ALA* 1.3 70.5 - - - +
600A CYS* 1.3 60.8 + - - +
601A CYS* 4.2 6.8 - - - -
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Residues in contact with CYS 600 (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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533A ASN 4.0 0.7 - - - +
534A CYS* 3.3 1.4 - - - -
535A SER* 2.7 53.1 + - - +
537A HIS* 3.8 24.9 - - - +
552A CYS* 2.0 54.3 - - + -
557A HIS* 4.4 9.8 - - + -
558A VAL 3.5 5.2 - - - +
598A ALA* 4.1 8.5 - - - -
599A SER* 1.3 75.1 + - - +
601A CYS* 1.3 61.4 + - - +
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Residues in contact with CYS 601 (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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484A LEU* 3.7 18.8 - - - -
529A LEU* 4.6 5.8 - - + -
532A ALA* 4.6 4.7 - - + -
533A ASN 3.3 2.9 - - - -
534A CYS* 2.0 46.2 - - - -
557A HIS* 3.2 4.7 - - - -
558A VAL* 2.8 41.1 + - + +
560A THR* 4.0 21.8 - - + -
599A SER* 4.2 2.2 - - - -
600A CYS* 1.3 76.1 - - - +
602A HIS* 1.3 62.5 + - - +
603A ALA* 3.3 5.3 + - + -
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Residues in contact with HIS 602 (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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531A GLN 3.7 4.6 + - - +
532A ALA* 3.2 6.9 - - - -
533A ASN* 2.6 51.4 + - + +
555A GLN 4.4 1.5 + - - -
556A GLY* 3.1 42.3 - - - -
557A HIS* 3.4 26.1 - + + +
601A CYS* 1.3 70.3 - - - +
603A ALA* 1.3 58.3 + - - +
604A PRO* 3.6 22.6 - - + +
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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