Contacts of the helix formed by residues 596 - 604 (chain A) in PDB entry 3UGM
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 596 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A HIS 5.7 3.1 - - - +
559A GLY 5.8 3.6 - - - +
560A LEU* 5.3 10.1 - - + -
585A LEU* 5.5 12.8 - - + -
589A CYS* 4.8 13.0 - - - -
595A THR* 1.4 88.2 - - - +
597A ASP* 1.4 64.0 + - - +
598A GLN 2.9 1.6 - - - -
599A VAL* 2.2 36.9 + - + +
600A VAL* 3.1 11.4 + - - +
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Residues in contact with ASP 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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564A GLN* 3.4 32.5 + - - +
595A THR* 3.5 4.0 + - - +
596A PRO* 1.4 80.3 - - - +
598A GLN* 1.3 61.5 + - - +
600A VAL* 3.2 8.3 + - - +
601A ALA* 3.0 21.2 + - - +
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Residues in contact with GLN 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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594A LEU* 3.7 16.3 - - + +
595A THR* 2.8 44.9 + - + +
596A PRO 2.7 2.0 + - - -
597A ASP* 1.3 76.0 - - - +
599A VAL* 1.4 59.5 + - - +
601A ALA* 3.3 15.8 + - - +
602A ILE* 3.1 19.7 - - - +
630A PRO* 5.8 0.7 - - - +
631A ASP* 5.1 5.7 - - - +
634A VAL* 3.0 53.3 - - - +
638A SER* 5.2 1.4 - - - -
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Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A VAL* 4.0 22.0 - - + -
584A LEU 5.9 0.2 - - - -
585A LEU* 4.7 24.0 - - + +
588A LEU* 4.5 16.8 - - + -
589A CYS* 5.1 0.7 - - - -
594A LEU* 4.3 16.6 - - + +
595A THR 3.3 17.5 - - - +
596A PRO* 2.2 24.6 + - + +
598A GLN* 1.4 67.1 - - - +
600A VAL* 1.3 66.5 + - + +
601A ALA 3.1 1.1 - - - -
602A ILE* 3.0 24.3 + - + +
603A ALA* 3.2 11.6 + - - +
612A LEU* 4.6 16.1 - - + +
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LEU* 3.3 35.0 - - + -
564A GLN* 3.5 52.0 - - + +
567A ALA* 5.9 1.6 - - + -
568A ILE* 4.1 14.8 - - + -
581A VAL* 5.3 1.6 - - + -
585A LEU* 6.2 0.4 - - + -
596A PRO 3.1 7.3 + - - +
597A ASP* 3.3 10.8 - - - +
599A VAL* 1.3 76.6 - - + +
601A ALA* 1.3 63.7 + - - +
603A ALA* 3.0 12.4 + - - +
604A SER* 3.0 25.6 + - - +
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Residues in contact with ALA 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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597A ASP 3.0 12.4 + - - +
598A GLN* 3.3 16.8 - - - +
599A VAL 3.1 0.6 - - - -
600A VAL* 1.3 76.4 - - - +
602A ILE* 1.3 58.5 + - - +
604A SER* 4.3 5.6 - - - -
605A ASN* 3.7 6.6 - - - +
638A SER* 3.3 34.5 - - - +
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Residues in contact with ILE 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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588A LEU* 5.5 1.1 - - + -
594A LEU* 4.0 16.6 - - + -
598A GLN* 3.1 35.4 - - - +
599A VAL* 3.0 16.3 + - + +
601A ALA* 1.3 76.2 - - - +
603A ALA* 1.3 64.0 + - - +
604A SER 3.4 0.7 - - - -
605A ASN* 4.3 11.0 + - - +
608A GLY* 4.0 12.1 - - - +
611A ALA* 4.7 10.2 - - + +
612A LEU* 3.6 28.3 - - + -
615A VAL* 4.8 5.8 - - + -
634A VAL* 4.7 1.8 - - + +
637A ALA* 2.7 46.9 - - + -
638A SER* 4.0 5.8 - - - +
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Residues in contact with ALA 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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568A ILE* 3.1 43.1 - - + +
571A HIS* 4.7 0.2 - - - -
577A ALA* 3.8 12.4 - - + +
581A VAL* 4.2 12.8 - - + -
599A VAL 3.2 10.4 + - - +
600A VAL 3.0 7.9 + - - +
602A ILE* 1.3 78.4 - - - +
604A SER* 1.3 56.6 + - - +
605A ASN 3.1 17.5 + - - +
608A GLY* 3.9 8.5 - - - -
612A LEU* 4.5 9.2 - - + +
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Residues in contact with SER 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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567A ALA* 3.1 27.0 + - - +
568A ILE* 3.4 14.1 - - - +
571A HIS* 2.6 32.0 + - - -
600A VAL* 3.0 22.2 + - - +
601A ALA* 4.3 4.7 + - - -
602A ILE 3.4 1.8 - - - -
603A ALA* 1.3 74.7 - - - +
605A ASN* 1.3 64.8 + - - +
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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