Contacts of the strand formed by residues 556 - 565 (chain A) in PDB entry 2P2F
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 GLY 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A ARG* 3.9 14.8 - - - -
388A GLU* 4.3 4.9 - - - -
521A ASN 4.4 1.3 - - - -
551A PRO* 3.5 7.6 - - - +
552A HIS 2.9 30.9 + - - +
554A ILE 3.4 3.6 + - - -
555A LYS* 1.3 72.6 - - - +
557A GLN* 1.3 62.1 + - - +
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Residues in contact with GLN 557 (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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519A VAL 4.6 1.8 + - - +
520A LEU* 3.6 14.8 - - - +
521A ASN* 2.9 44.5 + - + +
522A VAL* 3.5 26.9 - - + +
549A GLY* 3.4 27.2 + - - +
550A ILE 3.0 13.2 - - - +
551A PRO* 5.1 0.7 - - + -
552A HIS* 4.0 4.0 - - - +
555A LYS* 3.2 9.7 + - - +
556A GLY* 1.3 77.8 - - - +
558A ALA* 1.3 64.0 + - - +
616A ARG* 6.1 1.8 - - - +
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Residues in contact with ALA 558 (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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520A LEU* 4.8 0.2 - - - +
522A VAL* 4.7 3.4 - - - -
549A GLY* 3.4 8.0 - - - -
550A ILE* 2.9 42.5 + - + +
552A HIS* 3.9 22.3 - - + +
555A LYS* 4.7 3.1 - - - +
557A GLN* 1.3 75.6 - - - +
559A ILE* 1.3 66.6 + - - +
594A ASP* 3.3 31.6 - - + +
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Residues in contact with ILE 559 (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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520A LEU* 4.0 9.0 - - + -
522A VAL* 3.8 29.8 - - + -
527A LEU* 4.4 2.5 - - + -
532A ILE* 3.9 16.6 - - + -
547A VAL* 3.4 31.6 - - + -
548A VAL 3.8 2.7 - - - +
550A ILE* 5.6 0.4 - - - -
558A ALA* 1.3 73.8 - - - +
560A TYR* 1.3 60.4 + - - +
561A ALA 4.0 0.2 - - - -
590A LEU 4.2 5.2 - - - +
591A ALA* 3.8 31.6 - - - +
592A THR 3.8 9.6 - - - +
593A PRO* 3.5 22.3 - - + +
594A ASP* 2.7 35.6 + - - +
595A VAL* 3.3 5.8 + - - +
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Residues in contact with TYR 560 (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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546A ALA 4.0 0.3 - - - +
547A VAL* 3.7 0.9 - - - -
548A VAL* 3.1 33.2 + - + +
550A ILE* 3.7 31.0 - - + -
558A ALA 3.8 0.4 + - - -
559A ILE* 1.3 74.6 - - - +
561A ALA* 1.3 62.2 + - - +
562A TYR* 3.4 37.1 + + - -
595A VAL* 3.7 34.4 - - + +
597A HIS* 2.7 40.2 + - + +
619A ALA* 3.7 21.8 - - + -
645A LYS* 3.3 33.1 - - - +
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Residues in contact with ALA 561 (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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536A LEU* 3.8 29.4 - - + -
546A ALA 3.8 3.4 - - - -
547A VAL* 4.0 8.7 - - + -
559A ILE 4.0 0.2 - - - -
560A TYR* 1.3 74.8 - - - +
562A TYR* 1.3 56.8 + - - +
563A VAL* 4.0 3.5 + - + +
593A PRO* 4.2 9.2 - - + -
595A VAL 2.8 9.4 + - - +
596A LEU* 3.5 21.4 - - + -
597A HIS* 2.7 35.0 + - - +
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Residues in contact with TYR 562 (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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545A ALA* 3.1 8.9 - - - +
546A ALA 2.8 44.3 + - - +
548A VAL* 4.2 7.0 - - + -
560A TYR* 3.4 25.8 - + - -
561A ALA* 1.3 71.9 - - - +
563A VAL* 1.3 59.3 + - - +
597A HIS* 3.3 44.2 - + - +
599A THR* 4.5 3.6 - - + -
602A LEU* 3.9 18.6 - - + -
615A LEU* 2.8 63.0 + - + -
618A ILE* 3.5 21.1 - - + +
619A ALA 3.6 4.3 + - - -
641A LEU* 4.0 13.7 - - + -
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Residues in contact with VAL 563 (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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536A LEU* 4.3 9.0 - - + -
542A ILE* 3.7 37.5 - - + -
544A GLU 3.7 2.7 - - - -
545A ALA* 4.3 7.9 - - + -
561A ALA* 4.1 21.8 - - + +
562A TYR* 1.3 80.8 - - - +
564A THR* 1.3 62.0 + - - +
565A LEU* 4.0 7.7 + - + +
579A VAL* 5.3 0.2 - - + -
596A LEU* 4.3 13.7 - - + -
597A HIS 2.9 11.1 + - - +
598A TRP* 3.4 29.5 - - + +
599A THR* 2.7 32.0 + - - +
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Residues in contact with THR 564 (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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542A ILE* 3.6 2.3 - - - +
543A ALA* 2.7 34.0 + - + +
544A GLU* 2.8 39.3 + - - +
563A VAL* 1.3 76.1 - - - +
565A LEU* 1.3 61.8 + - - +
599A THR* 2.9 20.8 + - - +
600A ASP* 3.9 19.3 - - - +
602A LEU* 3.6 26.7 - - + +
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Residues in contact with LEU 565 (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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541A LYS* 3.4 16.8 - - + +
542A ILE* 4.1 7.9 - - + -
543A ALA* 4.0 2.5 - - - +
563A VAL* 4.0 21.9 + - + +
564A THR* 1.3 83.8 - - - +
566A ASN* 1.3 67.3 + - - +
567A HIS* 3.7 4.5 + - - -
569A GLU* 3.7 21.8 - - + +
570A GLU 4.0 4.5 - - - +
571A PRO* 3.9 28.7 - - + -
575A LEU* 3.8 27.8 - - + -
579A VAL* 5.9 0.7 - - + -
598A TRP* 4.0 20.2 - - + -
599A THR 4.6 0.6 + - - -
600A ASP* 4.5 7.9 + - - +
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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