Contacts of the helix formed by residues 617 - 626 (chain A) in PDB entry 1M2V
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 ASP 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU* 4.9 10.1 - - - +
36A LEU* 3.7 7.6 - - + -
38A THR* 4.7 4.9 - - - +
453A TYR 5.3 0.2 + - - -
455A SER* 3.6 17.8 + - - +
616A GLU* 1.3 76.1 + - - +
618A THR* 1.3 60.3 + - - +
619A THR* 3.9 14.7 + - - -
620A ASN* 3.0 35.5 + - - +
621A SER* 2.5 38.0 + - - -
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Residues in contact with THR 618 (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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7A GLU* 3.9 7.1 + - - -
13A ARG* 3.6 52.2 - - - +
36A LEU* 3.4 18.7 - - + +
526A GLU* 4.1 18.4 - - + +
527A ALA* 4.2 6.3 - - - +
530A VAL* 3.9 19.1 - - + -
617A ASP* 1.3 73.4 - - - +
619A THR* 1.3 66.3 + - - +
621A SER* 3.4 1.2 + - - -
622A LEU* 3.1 30.0 + - + +
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Residues in contact with THR 619 (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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4A GLU* 5.6 1.7 + - - -
7A GLU* 4.9 10.1 + - - -
13A ARG* 5.2 3.7 + - - +
617A ASP* 3.5 12.6 + - - -
618A THR* 1.3 81.9 - - - +
620A ASN* 1.3 72.9 + - - +
622A LEU* 3.4 16.0 + - - +
623A ILE* 3.5 19.8 + - + +
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Residues in contact with ASN 620 (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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453A TYR* 5.7 3.6 - - - -
616A GLU* 3.1 45.5 + - + -
617A ASP* 3.0 13.9 + - - +
619A THR* 1.3 87.0 - - - +
621A SER* 1.3 65.1 + - - +
623A ILE* 3.2 18.4 + - - +
624A MET* 3.1 24.6 + - - +
659A PHE* 3.8 22.4 - - + -
705A ARG* 5.2 5.7 + - - +
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Residues in contact with SER 621 (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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530A VAL* 3.5 29.9 - - - +
613A PHE* 3.6 21.8 + - - -
616A GLU* 3.5 15.8 + - - +
617A ASP 2.5 26.7 + - - -
620A ASN* 1.3 76.2 - - - +
622A LEU* 1.3 64.1 + - - +
624A MET* 2.9 22.9 + - - +
625A ILE* 3.0 17.7 + - - +
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Residues in contact with LEU 622 (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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13A ARG* 5.8 0.2 - - - +
526A GLU* 3.3 49.8 - - + +
529A ALA* 4.6 0.7 - - + -
530A VAL* 4.0 16.2 - - + -
586A PHE* 3.6 38.8 - - + -
618A THR* 3.1 23.0 + - + +
619A THR* 3.6 9.9 - - - +
620A ASN 3.2 0.2 - - - -
621A SER* 1.3 74.2 - - - +
623A ILE* 1.3 60.0 + - + +
625A ILE* 2.9 10.7 + - + +
626A GLN* 2.6 37.3 + - - +
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Residues in contact with ILE 623 (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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619A THR* 3.5 18.4 + - + +
620A ASN* 3.2 20.7 + - - +
622A LEU* 1.3 76.4 - - + +
624A MET* 1.3 63.2 + - - +
626A GLN 3.6 7.4 - - - -
627A PRO* 3.4 21.8 - - + +
628A THR* 4.6 15.3 - - + +
657A ASP* 3.0 55.8 - - + +
658A THR 4.0 2.0 - - - +
659A PHE* 3.8 12.6 - - + +
701A LEU* 5.4 4.9 - - + -
705A ARG* 4.0 10.8 - - - +
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Residues in contact with MET 624 (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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593A SER* 4.3 4.9 - - - -
594A GLN* 5.4 4.0 + - - +
595A PHE* 3.8 16.1 - - + -
612A ILE* 4.0 3.1 - - + -
613A PHE* 3.7 34.1 - - + -
616A GLU* 3.5 36.6 - - + -
620A ASN 3.1 24.0 + - - +
621A SER* 2.9 16.6 + - - +
623A ILE* 1.3 79.8 - - - +
625A ILE* 1.3 60.2 + - - +
627A PRO* 4.4 5.0 - - - +
658A THR* 4.1 9.0 - - - +
659A PHE* 3.8 25.4 - - + -
660A PHE* 3.4 38.9 - - + -
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Residues in contact with ILE 625 (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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529A ALA* 4.0 30.7 - - + +
530A VAL* 4.5 2.7 - - - -
533A ALA* 4.2 10.3 - - + -
586A PHE* 3.3 32.8 - - + +
589A TYR* 3.6 18.7 - - + +
590A LEU* 3.4 21.3 - - + +
593A SER* 4.4 5.5 - - - -
595A PHE* 4.3 10.8 - - + -
613A PHE* 4.2 13.2 - - + -
621A SER 3.0 16.9 + - - +
622A LEU* 2.9 20.7 + - + +
624A MET* 1.3 78.6 - - - +
626A GLN* 1.3 61.2 + - + +
627A PRO* 3.1 10.7 - - - +
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Residues in contact with GLN 626 (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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585A GLN* 3.1 35.2 + - - +
586A PHE* 3.7 27.4 - - + -
589A TYR* 2.9 47.2 - - + -
622A LEU 2.6 20.5 + - - +
623A ILE* 3.6 6.2 - - - +
625A ILE* 1.3 74.3 - - - +
627A PRO* 1.3 72.0 - - - +
628A THR* 3.7 5.4 + - - +
643A LEU* 4.0 6.0 - - + +
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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