Contacts of the helix formed by residues 594 - 605 (chain A) in PDB entry 3U44
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 TRP 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A THR* 4.0 21.5 + - - -
548A VAL* 3.5 39.9 - - + +
551A GLU* 4.0 24.9 - - + -
589A LEU* 4.3 15.2 - - + +
593A PRO* 1.3 90.6 - - + +
595A ALA* 1.3 67.4 + - - +
596A PRO* 3.3 3.6 - - - -
597A GLN* 3.0 11.7 + - - +
598A ILE* 2.8 43.9 + - + +
807A ALA* 5.7 0.7 - - + -
808A GLY* 3.9 28.3 - - - -
811A ARG* 4.1 37.7 - - + +
883A SER* 4.9 4.9 - - - -
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Residues in contact with ALA 595 (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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589A LEU* 4.0 5.6 - - - +
592A MET* 3.5 40.1 - - + +
594A TRP* 1.3 76.8 - - - +
596A PRO* 1.3 68.7 - - + +
599A MET* 3.0 30.3 + - - +
611A ALA* 4.7 3.1 - - + -
613A LEU* 4.4 12.8 - - + -
790A LEU* 3.4 20.6 - - + +
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Residues in contact with PRO 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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592A MET 4.0 5.6 - - - +
593A PRO* 3.6 17.7 - - + +
594A TRP 3.3 1.6 - - - -
595A ALA* 1.3 98.2 - - + +
597A GLN* 1.3 69.9 + - + +
599A MET* 3.4 19.8 + - + +
600A GLU* 3.2 20.6 + - - +
613A LEU* 4.8 10.3 - - + -
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Residues in contact with GLN 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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545A LEU* 3.2 28.9 - - - +
548A VAL* 3.0 38.2 - - + +
549A GLN* 3.7 13.8 + - + +
593A PRO 4.7 8.4 - - - +
594A TRP* 3.0 10.7 + - - +
596A PRO* 1.3 79.7 - - + +
598A ILE* 1.3 69.6 + - - +
600A GLU* 3.2 24.4 + - - +
601A GLU* 3.7 6.6 + - - +
1114B LYS* 5.5 1.4 + - - -
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Residues in contact with ILE 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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548A VAL* 3.2 30.5 - - + +
551A GLU* 6.3 0.9 - - + -
552A ALA* 3.7 22.9 - - + -
555A ILE* 5.5 7.0 - - + -
587A ILE* 3.8 6.7 - - + -
589A LEU* 4.6 10.8 - - + -
594A TRP* 2.8 49.9 + - + +
595A ALA 3.7 2.5 - - - +
597A GLN* 1.3 74.6 - - - +
599A MET* 1.3 65.6 + - - +
600A GLU 3.0 1.0 + - - -
601A GLU* 3.4 2.9 + - - +
602A LEU* 3.2 47.4 + - + +
790A LEU* 3.7 21.1 - - + -
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Residues in contact with MET 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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595A ALA 3.0 18.8 + - - +
596A PRO* 3.5 27.1 - - + +
598A ILE* 1.3 78.9 - - - +
600A GLU* 1.3 63.4 - - - +
603A ARG* 3.0 39.5 + - - +
609A VAL* 3.2 45.3 - - + +
611A ALA* 3.5 31.9 - - - +
613A LEU* 4.1 25.4 - - + -
790A LEU* 3.9 6.5 - - + -
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Residues in contact with GLU 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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596A PRO 3.2 8.0 + - - +
597A GLN* 3.2 18.1 + - - +
598A ILE 3.0 1.6 + - - -
599A MET* 1.3 77.2 - - - +
601A GLU* 1.3 60.1 + - + +
603A ARG* 2.8 33.9 - - + +
604A ALA* 2.8 11.2 + - + +
1134B GLU* 5.4 11.2 - - - +
1135B SER* 5.7 8.5 - - - +
1137B GLU* 4.7 9.9 - - - +
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Residues in contact with GLU 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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549A GLN* 3.3 15.2 - - - +
552A ALA* 3.0 17.2 - - + +
553A LYS* 2.7 73.9 + - - +
597A GLN 3.7 4.4 + - - +
598A ILE 3.4 8.4 + - - +
600A GLU* 1.3 78.6 - - + +
602A LEU* 1.3 66.8 + - + +
604A ALA* 2.9 30.5 + - + +
605A GLN* 3.2 19.4 + - - +
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Residues in contact with LEU 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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552A ALA* 3.5 15.3 - - + +
555A ILE* 5.0 4.5 - - + -
556A ALA* 3.2 39.5 - - + +
559A ILE* 4.9 4.5 - - + -
587A ILE* 3.4 24.2 - - + -
598A ILE* 3.2 40.7 + - + +
601A GLU* 1.3 80.3 - - + +
603A ARG* 1.3 56.1 + - - +
605A GLN* 3.3 13.8 - - - +
607A ILE* 2.9 17.0 - - - +
609A VAL* 3.2 24.5 - - + -
788A VAL* 4.5 9.6 - - + +
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Residues in contact with ARG 603 (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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599A MET* 3.0 37.1 + - - +
600A GLU* 2.8 26.8 - - + +
602A LEU* 1.3 75.7 - - - +
604A ALA* 1.3 65.5 + - - +
605A GLN 3.1 3.2 + - - -
606A GLY 3.9 8.1 + - - +
607A ILE 3.6 8.1 - - - -
608A PRO* 3.7 22.4 - - + +
609A VAL 3.4 26.6 + - - +
732A GLY* 4.9 16.4 - - - +
735B ARG* 6.2 2.2 - - - +
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Residues in contact with ALA 604 (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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600A GLU* 2.8 7.8 + - + +
601A GLU* 2.9 28.4 + - + +
603A ARG* 1.3 80.0 - - - +
605A GLN* 1.3 67.3 + - - +
606A GLY 4.3 0.2 - - - -
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Residues in contact with GLN 605 (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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553A LYS* 4.7 19.8 - - - +
556A ALA* 4.4 11.9 - - + +
560A ARG* 3.1 50.4 + - - +
601A GLU* 3.3 16.5 + - - +
602A LEU 3.3 14.8 - - - +
604A ALA* 1.3 91.8 - - - +
606A GLY* 1.3 61.8 + - - +
607A ILE* 4.0 0.7 + - - +
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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