Contacts of the helix formed by residues 592 - 598 (chain A) in PDB entry 5C58
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 ALA 592 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A TYR* 3.5 39.9 - - + +
484A ARG* 3.9 13.7 - - - +
514A LEU* 3.5 2.3 - - - +
589A ARG* 4.6 1.3 - - - +
590A PRO 3.7 1.2 + - - -
591A PRO* 1.3 73.5 - - - +
593A ILE* 1.3 65.4 + - - +
594A THR 3.3 3.1 - - - +
595A GLU* 2.8 20.7 + - + +
596A THR* 2.8 27.4 + - - -
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Residues in contact with ILE 593 (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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432A LEU* 4.6 3.8 - - + -
464A ASP* 4.3 15.0 - - + -
466A ALA* 4.2 22.4 - - + +
479A THR 6.0 0.2 - - - -
480A PRO* 4.1 5.1 - - + +
481A ALA 4.3 2.2 - - - -
482A GLY* 4.1 17.9 - - - +
483A ASN* 3.8 9.0 - - - +
484A ARG* 3.6 41.1 - - + +
514A LEU* 3.8 11.7 - - + -
592A ALA* 1.3 73.5 - - - +
594A THR* 1.3 59.8 + - - +
596A THR 3.5 0.3 + - - -
597A LEU* 3.0 52.3 + - + +
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Residues in contact with THR 594 (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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170A TYR* 3.3 31.2 - - - +
185A GLN* 2.6 30.3 + - - +
187A SER* 4.0 9.2 - - - +
478A VAL 4.8 0.2 - - - +
479A THR* 3.1 27.3 + - - +
592A ALA* 3.3 1.2 - - - +
593A ILE* 1.3 79.5 - - - +
595A GLU* 1.3 62.8 + - - +
596A THR 3.0 0.2 + - - -
598A THR* 2.9 41.6 + - - -
608A GLN* 4.9 0.9 - - - +
676A TYR* 4.5 6.7 - - + +
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Residues in contact with GLU 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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170A TYR* 3.4 23.2 - - + -
172A ARG* 5.3 0.3 + - - -
589A ARG* 3.0 23.7 + - - -
591A PRO* 3.3 6.6 - - - +
592A ALA* 2.8 41.6 + - + +
594A THR* 1.3 75.8 - - - +
596A THR* 1.3 59.0 + - - +
598A THR* 4.6 2.9 - - - +
609A TYR 5.0 0.2 - - - +
610A PRO 4.8 0.2 - - - -
611A ASN* 4.0 9.5 + - - +
614A LEU* 3.4 19.5 - - + +
655A ILE* 3.5 21.3 - - - +
676A TYR* 3.4 46.4 + - + +
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Residues in contact with THR 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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514A LEU* 3.4 23.2 - - + +
556A VAL* 4.3 7.9 - - + -
558A ARG* 4.8 4.5 - - - +
591A PRO* 3.4 18.4 - - - +
592A ALA 2.8 22.8 + - - -
593A ILE 3.9 1.8 - - - -
594A THR 3.0 0.6 - - - -
595A GLU* 1.3 80.7 - - - +
597A LEU* 1.3 74.9 + - + +
598A THR 3.7 0.7 - - - -
610A PRO* 3.4 5.0 - - - +
611A ASN 3.0 39.9 + - - +
612A PRO* 3.8 13.6 - - + +
614A LEU* 4.3 1.1 - - + +
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Residues in contact with LEU 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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480A PRO* 3.2 14.7 - - + +
481A ALA 3.7 16.2 - - - +
514A LEU* 4.7 4.0 - - + -
515A ARG 4.1 5.6 - - - +
516A GLY* 3.7 29.4 - - - +
517A GLN 4.4 1.8 - - - +
518A THR* 2.8 39.1 + - + -
556A VAL* 3.6 35.0 - - + -
593A ILE* 3.0 31.6 + - + +
596A THR* 1.3 88.5 - - + +
598A THR* 1.3 66.1 + - - +
599A ASN* 3.0 8.0 - - - +
610A PRO* 4.1 0.2 - - - -
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Residues in contact with THR 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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477A GLY 4.2 0.7 - - - -
478A VAL* 2.9 24.0 + - - +
479A THR 3.8 2.5 - - - -
480A PRO* 3.6 10.2 - - - +
594A THR* 2.9 22.6 + - - +
595A GLU 4.6 3.1 - - - +
596A THR 3.7 0.2 - - - -
597A LEU* 1.3 78.1 - - - +
599A ASN* 1.3 60.2 + - - +
600A GLY 4.3 1.2 + - - -
608A GLN* 2.9 32.8 + - + +
609A TYR 3.1 17.1 - - - +
610A PRO* 3.0 26.9 - - + +
676A TYR* 4.3 14.6 - - + -
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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