Contacts of the helix formed by residues 545 - 554 (chain A) in PDB entry 2IVF
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 PRO 545 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A VAL* 1.3 90.1 - - + +
546A PRO* 1.3 71.1 - - + +
547A ALA* 3.4 2.7 - - + +
548A MET* 3.4 30.8 + - + +
549A TRP 4.4 1.4 + - - -
587A TRP* 4.2 12.1 - - + -
591A HIS* 3.7 31.6 - - + +
954A TYR* 3.6 21.2 - - + -
960A SER* 3.3 30.1 - - - +
961A PRO* 5.1 2.2 - - + -
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Residues in contact with PRO 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PRO* 4.0 13.2 - - + -
216A ASP* 3.7 7.4 - - + +
219A VAL* 3.5 36.1 - - + +
220A ASP* 3.6 42.2 - - + +
544A VAL 3.2 8.0 - - - +
545A PRO* 1.3 79.1 - - + +
547A ALA* 1.3 64.2 + - - +
548A MET 3.1 3.1 + - - -
549A TRP* 3.1 27.9 - - + +
550A LEU* 3.3 15.7 - - + +
963A PRO* 4.4 3.8 - - + -
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Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PRO* 3.4 2.3 - - + +
546A PRO* 1.3 81.0 - - - +
548A MET* 1.3 60.5 + - + +
551A TYR* 2.9 32.6 + - - +
560A TRP* 3.3 24.0 - - + -
574A PHE* 4.2 10.7 - - + -
940A PRO* 4.5 3.1 - - + -
961A PRO* 3.4 39.6 + - + +
963A PRO* 4.6 3.5 - - + +
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Residues in contact with MET 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PRO* 3.7 23.3 - - + +
546A PRO 3.1 1.6 + - - -
547A ALA* 1.3 82.6 - - + +
549A TRP* 1.3 59.0 + - - +
551A TYR* 3.5 1.6 - - - +
552A TYR* 2.9 37.9 + - + -
574A PHE* 5.6 1.6 - - - -
578A LEU* 3.7 38.4 - - + -
587A TRP* 3.8 39.5 - - + -
591A HIS 3.8 20.4 - - - +
592A ILE* 3.8 25.6 - - + -
593A ARG 4.8 1.6 - - - +
945A LEU* 4.1 12.1 - - + -
961A PRO* 5.2 2.9 - - + -
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Residues in contact with TRP 549 (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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187A ILE* 3.6 27.8 - - + -
189A ASP* 3.4 25.4 + - - -
215A PRO* 3.3 33.3 - - + +
220A ASP* 5.3 1.0 + - - -
544A VAL* 5.5 0.4 - - + -
545A PRO 4.4 1.3 + - - -
546A PRO* 3.1 32.4 + - + +
548A MET* 1.3 76.1 - - - +
550A LEU* 1.3 79.8 + - + +
553A HIS* 2.7 53.0 + - + +
554A VAL* 3.5 23.0 + - + -
593A ARG 3.4 21.5 - - - +
594A PRO* 3.7 11.2 - - + -
600A PRO* 4.7 0.4 - - + -
603A TYR* 3.9 12.6 - + - -
614A LYS* 4.9 0.4 - - - -
621A PHE* 4.1 2.2 - + - -
625A LEU* 3.7 33.0 - - + -
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Residues in contact with LEU 550 (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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220A ASP* 4.4 11.4 - - - +
546A PRO 3.3 19.0 + - - +
548A MET 3.3 0.6 - - - -
549A TRP* 1.3 105.5 - - + +
551A TYR* 1.3 56.9 + - - +
554A VAL* 3.1 34.5 + - + -
555A GLY 3.4 0.5 + - - -
556A TYR* 3.3 30.8 + - + +
560A TRP* 3.7 26.9 - - + -
614A LYS* 4.5 12.8 - - + -
621A PHE* 3.9 18.2 - - + -
963A PRO* 4.0 19.1 - - + -
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Residues in contact with TYR 551 (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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547A ALA 2.9 20.6 + - - +
548A MET* 3.5 5.4 - - - +
550A LEU* 1.3 80.0 - - - +
552A TYR* 1.3 90.0 + + - +
553A HIS 3.8 0.2 + - - -
555A GLY 4.3 0.9 + - - -
556A TYR 4.1 0.9 + - - -
557A ASP* 3.3 60.8 + - + +
560A TRP* 3.9 12.2 - + + -
561A ASN* 3.0 30.7 + - - -
574A PHE* 3.8 24.9 - + + -
575A GLY* 3.4 17.4 + - - -
578A LEU* 3.8 14.8 - - + -
579A ASP* 5.5 1.7 + - - -
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Residues in contact with TYR 552 (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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548A MET* 2.9 28.8 + - - +
551A TYR* 1.3 102.4 - + - +
553A HIS* 1.3 80.3 + - + +
555A GLY 5.0 0.7 - - - -
578A LEU* 3.6 16.5 - - + +
579A ASP* 4.7 4.5 + - - -
582A LYS* 3.4 28.3 + - - +
592A ILE* 3.7 34.5 - - + -
594A PRO 5.7 0.2 - - - -
596A PRO* 3.7 29.5 - - + +
628A LYS* 4.8 2.8 + - - -
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Residues in contact with HIS 553 (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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549A TRP* 2.7 40.0 + - + +
552A TYR* 1.3 82.6 + - + +
554A VAL* 1.3 61.6 + - + +
555A GLY 3.5 2.2 - - - -
594A PRO* 2.8 35.4 + - + +
595A ALA 3.1 10.9 + - - -
596A PRO* 3.9 15.4 - - + +
598A LYS 2.9 30.5 + - - -
599A THR* 4.8 0.2 - - - -
600A PRO* 3.5 27.5 - - + +
624A VAL* 3.8 4.4 - - - +
625A LEU* 4.6 1.9 - - - +
628A LYS* 2.8 36.2 + - - +
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A TRP* 3.6 35.0 - - + -
550A LEU* 3.1 25.4 + - + +
553A HIS* 1.3 80.9 - - - +
555A GLY* 1.3 61.1 + - - +
556A TYR* 3.3 19.1 + - + -
620A MET* 3.5 32.8 - - - +
621A PHE* 3.7 21.8 - - + -
624A VAL* 3.5 13.1 - - - +
625A LEU* 4.0 14.1 - - + -
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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