Contacts of the strand formed by residues 618 - 623 (chain A) in PDB entry 1MPX
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 618 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A VAL* 3.4 4.4 - - - -
444A SER 2.9 31.1 + - - -
508A THR* 3.5 11.2 - - - +
509A SER* 3.5 9.4 - - - +
510A GLY* 4.1 6.7 - - - +
601A GLN* 3.5 24.5 - - + +
617A LYS* 1.3 77.7 - - - +
619A THR* 1.3 63.6 + - - +
620A GLN* 3.5 18.8 + - - +
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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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441A GLU* 3.4 41.3 - - + +
442A TYR 3.8 4.3 - - - +
443A VAL* 4.0 15.5 - - + +
507A SER* 3.9 0.7 + - - +
508A THR* 3.5 2.6 - - - -
509A SER* 2.9 41.0 + - - -
618A ALA* 1.3 70.7 - - - +
620A GLN* 1.3 58.9 + - - +
621A ARG* 4.8 9.0 - - - +
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Residues in contact with GLN 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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440A GLU 3.9 0.4 - - - +
441A GLU* 3.3 5.9 - - - +
442A TYR* 2.7 77.2 + - + +
444A SER* 3.9 8.3 - - - -
507A SER 3.4 2.7 - - - -
508A THR* 2.6 33.7 + - - -
513A SER* 2.9 22.7 + - - -
515A TRP* 3.7 12.6 - - + -
590A SER* 3.1 19.4 + - - +
601A GLN* 4.0 1.7 - - - +
618A ALA* 3.5 16.5 - - - +
619A THR* 1.3 79.0 - - - +
621A ARG* 1.3 63.7 + - - +
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Residues in contact with ARG 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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439A PHE* 3.3 47.2 - - + -
440A GLU 3.3 3.8 - - - -
441A GLU* 2.9 25.5 + - + +
506A ALA* 3.1 7.7 - - - +
507A SER* 2.9 46.7 + - - +
515A TRP* 5.5 0.2 - - - -
619A THR* 4.8 8.5 - - - +
620A GLN* 1.3 80.2 - - - +
622A VAL* 1.3 62.9 + - - +
623A TYR* 3.8 24.6 + - + -
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Residues in contact with VAL 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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421A LEU* 4.0 19.7 - - + -
439A PHE* 3.3 2.2 - - - -
440A GLU* 2.9 28.3 + - - +
442A TYR* 4.2 7.6 - - + -
483A LEU* 3.6 28.9 - - + -
485A PHE* 4.5 7.9 - - + -
504A LEU* 3.8 16.6 - - + -
505A GLN 3.7 2.9 - - - -
506A ALA* 4.6 4.9 - - + -
515A TRP* 4.9 2.9 - - + -
588A VAL* 4.0 20.9 - - + -
621A ARG* 1.3 74.0 - - - +
623A TYR* 1.3 64.1 + - - +
624A VAL* 3.7 5.0 + - + +
630A SER* 3.7 17.9 - - - +
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Residues in contact with TYR 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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438A GLY* 3.4 18.4 - - - -
439A PHE* 3.8 20.6 - + + -
505A GLN* 2.8 24.3 + - + +
506A ALA* 4.3 1.1 - - - -
507A SER* 3.6 22.0 + - - -
562A ASN 5.4 1.6 + - - -
564A PRO* 3.6 37.0 - - + +
621A ARG* 3.8 35.4 + - + -
622A VAL* 1.3 71.9 - - - +
624A VAL* 1.3 58.6 + - - +
625A SER* 4.7 4.3 - - - -
628A GLN* 3.3 34.8 - - + +
630A SER* 2.7 35.7 + - - -
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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