Contacts of the strand formed by residues 595 - 599 (chain A) in PDB entry 6M0X
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 PHE 595 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 5.2 0.7 + - - -
565A LYS* 5.1 6.4 + - + -
583A ILE* 3.7 28.9 - - + -
587A ASP* 3.5 17.7 - - + -
588A LEU* 3.4 36.6 - - + -
591A ASN 3.4 19.1 - - - -
592A SER 3.4 16.8 + - - +
593A ASN* 3.0 4.3 - - - +
594A GLN* 1.3 102.2 - - + +
596A GLU* 1.3 71.1 + - - +
616A LEU* 3.8 15.9 - - + -
617A VAL 3.4 15.5 - - - +
618A TYR* 3.9 32.1 - + - -
619A ALA 3.8 0.9 - - - +
13C T 4.4 7.6 - - - +
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Residues in contact with GLU 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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120A TYR* 6.1 0.4 - - - +
565A LYS* 6.0 0.9 - - - +
593A ASN 5.2 1.2 - - - +
595A PHE* 1.3 82.0 - - - +
597A VAL* 1.3 64.5 + - - +
598A ASP 3.5 2.4 + - - -
615A VAL 3.9 0.2 - - - +
616A LEU* 4.1 4.0 - - - +
617A VAL* 3.1 30.9 + - - +
619A ALA* 3.6 26.0 - - + +
622A ASN* 2.6 40.6 + - + +
623A GLN* 3.2 18.8 - - - +
18B G 5.2 2.6 + - - -
12C C 3.3 32.2 + - - +
13C T 3.3 11.6 - - - +
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Residues in contact with VAL 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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565A LYS* 4.5 28.7 - - + +
568A LEU* 4.3 15.5 - - + -
596A GLU* 1.3 71.4 - - - +
598A ASP* 1.3 62.7 + - - +
599A ALA 3.7 1.6 + - - -
614A LYS* 3.6 41.5 - - + -
615A VAL 3.7 6.7 - - - +
616A LEU* 4.8 5.8 - - + -
12C C 3.7 17.8 + - - +
13C T 2.6 24.9 + - - +
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Residues in contact with ASP 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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578A TYR* 2.7 39.9 + - + -
596A GLU 3.5 3.0 + - - -
597A VAL* 1.3 74.0 - - - +
599A ALA* 1.3 82.4 + - - +
600A ILE* 3.3 2.4 - - - -
614A LYS* 3.3 7.7 - - - -
615A VAL* 3.1 35.3 + - + +
617A VAL* 4.2 5.2 - - + -
622A ASN* 3.0 28.7 - - - +
625A LYS* 3.2 14.1 + - - +
626A GLY 5.2 1.7 - - - +
11C C 4.5 0.9 - - - +
12C C 3.2 8.5 + - - -
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Residues in contact with ALA 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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597A VAL 3.7 1.4 + - - -
598A ASP* 1.3 85.4 - - - +
600A ILE* 1.3 68.0 + - - +
601A LEU 3.5 16.5 + - - +
602A PRO* 3.8 4.9 - - + +
603A LEU* 4.2 24.7 - - + +
608A ASP 5.4 0.2 - - - +
613A ASN* 3.3 14.6 - - - +
614A LYS* 5.5 3.6 - - + +
625A LYS* 3.3 2.1 + - - -
12C C 2.7 18.9 + - - +
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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