Contacts of the helix formed by residues 555 - 566 (chain A) in PDB entry 4BL8
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 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A ALA* 3.3 25.8 + - - -
554A TRP* 1.3 111.4 + - - +
556A GLY* 1.3 61.2 + - - +
557A GLN* 4.2 6.7 - - + +
558A GLY* 2.4 39.5 + - - +
559A ILE* 3.5 9.4 - - - +
602A ASP* 3.8 11.5 + - - +
605A ASN* 3.8 13.9 - - - +
92B PRO* 6.0 3.6 - - - +
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Residues in contact with GLY 556 (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 GLY* 3.2 25.2 + - - -
500A HIS* 6.0 1.1 - - - -
518A LEU* 4.7 4.0 - - - +
551A ALA* 3.9 13.2 + - - -
555A ASN* 1.3 73.2 - - - +
557A GLN* 1.3 65.6 + - - +
559A ILE* 3.4 3.5 + - - +
560A LEU* 3.1 34.0 + - - +
605A ASN* 4.7 3.0 - - - +
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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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497A SER* 2.9 48.1 + - - -
498A GLY* 3.3 7.6 - - - +
520A THR* 5.0 1.9 + - - -
521A GLU* 5.6 0.2 + - - -
555A ASN* 3.5 6.8 + - + +
556A GLY* 1.3 77.6 - - - +
558A GLY* 1.3 63.4 - - - +
560A LEU* 3.1 14.6 + - - +
561A GLU* 3.0 31.4 + - - +
564A ARG* 5.1 5.7 + - - -
92B PRO* 5.3 9.4 - - + -
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Residues in contact with GLY 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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554A TRP* 3.6 26.1 - - - -
555A ASN* 2.4 27.6 + - - +
557A GLN* 1.3 75.2 - - - +
559A ILE* 1.3 59.1 + - - -
561A GLU* 3.4 22.6 + - - +
562A LEU* 3.4 17.3 + - - +
92B PRO* 6.0 1.3 - - - +
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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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518A LEU* 3.9 22.4 - - + -
547A GLU* 4.3 17.7 - - + +
550A SER* 3.3 25.6 - - - +
551A ALA* 3.6 17.3 - - + +
554A TRP* 4.0 18.4 - - + -
555A ASN* 3.5 18.9 + - - +
556A GLY 3.4 4.3 + - - +
557A GLN 3.3 0.4 - - - -
558A GLY* 1.3 73.2 - - - +
560A LEU* 1.3 64.7 + - - +
562A LEU* 3.1 11.1 + - + +
563A LEU* 3.0 28.3 + - + +
584A ILE* 4.9 6.1 - - + -
585A PHE* 4.7 3.4 - - + -
595A VAL* 4.0 11.9 - - + -
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Residues in contact with LEU 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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498A GLY* 4.1 5.2 - - - -
518A LEU* 4.0 27.8 - - + -
519A LEU 3.5 20.6 - - - +
520A THR* 3.7 30.5 - - + +
541A VAL* 4.3 7.4 - - + -
556A GLY* 3.1 27.3 + - - +
557A GLN* 3.4 18.4 - - - +
559A ILE* 1.3 76.1 - - - +
561A GLU* 1.3 63.3 + - - +
563A LEU* 3.2 20.6 + - + +
564A ARG* 3.2 31.8 + - - +
574A LEU* 3.8 9.7 - - + +
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Residues in contact with GLU 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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554A TRP* 4.7 0.7 - - - -
557A GLN* 3.0 20.6 + - + +
558A GLY* 3.4 19.7 - - - +
559A ILE 3.2 0.2 - - - -
560A LEU* 1.3 75.9 - - - +
562A LEU* 1.3 67.2 + - + +
564A ARG* 3.3 30.5 + - - +
565A THR* 3.3 17.6 - - - +
594A ARG* 4.3 14.6 + - - -
92B PRO* 3.3 38.1 - - - +
93B PHE* 4.1 17.1 + - + +
96B ASP* 5.2 2.6 - - - +
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Residues in contact with LEU 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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554A TRP* 4.6 5.2 - - + -
558A GLY 3.5 15.7 - - - +
559A ILE* 3.1 13.7 + - + +
561A GLU* 1.3 77.2 - - + +
563A LEU* 1.3 65.7 + - - +
564A ARG 2.9 1.8 - - - -
565A THR* 2.9 27.8 + - + +
566A VAL* 3.3 10.4 + - - +
584A ILE* 4.0 24.5 - - + -
585A PHE* 4.8 0.4 - - + -
591A LEU* 4.5 31.2 - - + +
594A ARG* 4.8 21.5 - - + +
595A VAL* 3.9 27.4 - - + -
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Residues in contact with LEU 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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518A LEU* 4.2 12.8 - - + -
541A VAL* 4.1 17.9 - - + -
542A GLY 5.1 0.2 - - - +
543A VAL* 3.7 25.4 - - + -
547A GLU* 4.0 17.0 - - - +
559A ILE* 3.0 20.5 + - + +
560A LEU* 3.2 8.7 + - + +
562A LEU* 1.3 76.4 - - - +
564A ARG* 1.3 55.7 + - - +
566A VAL 3.1 23.2 - - - +
569A ALA* 4.1 16.6 - - + +
570A GLY 3.7 2.9 + - - -
571A GLY 3.2 9.4 + - - -
574A LEU* 3.6 15.9 - - + -
580A ARG* 4.5 2.2 - - - +
584A ILE* 3.6 31.0 - - + -
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Residues in contact with ARG 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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520A THR* 3.4 24.0 + - - -
521A GLU 5.2 3.4 + - - -
557A GLN* 5.1 5.7 + - - -
560A LEU* 3.2 18.3 + - - +
561A GLU* 3.3 37.4 - - - +
562A LEU 2.9 0.8 - - - -
563A LEU* 1.3 78.9 - - - +
565A THR* 1.3 61.8 + - + +
566A VAL 3.3 0.2 - - - -
567A PRO* 4.6 0.9 - - - +
571A GLY* 3.2 34.9 - - - +
572A PRO* 3.8 24.4 + - + +
574A LEU* 3.5 24.6 - - + +
326B GLN* 5.2 8.1 - - - +
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Residues in contact with THR 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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561A GLU* 3.3 16.8 - - + +
562A LEU* 2.9 23.3 + - + +
564A ARG* 1.3 78.1 - - + +
566A VAL* 1.3 64.1 + - - +
567A PRO* 3.4 10.1 - - - +
591A LEU* 4.8 10.6 - - - +
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Residues in contact with VAL 566 (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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562A LEU 3.3 13.3 + - - +
563A LEU 3.1 14.7 - - - +
564A ARG 3.3 0.4 - - - -
565A THR* 1.3 83.0 - - - +
567A PRO* 1.3 67.5 - - + +
568A ILE* 4.2 9.0 - - + -
569A ALA* 3.0 30.6 + - + -
570A GLY 3.4 0.5 + - - -
571A GLY 4.2 0.4 - - - -
584A ILE* 4.3 12.1 - - + +
587A ILE* 4.1 30.1 - - + -
588A ASP* 5.1 7.9 - - + +
591A LEU* 4.0 25.1 - - + -
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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