Contacts of the strand formed by residues 501 - 508 (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 ASP 501 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ASP* 4.6 9.1 - - - +
499A ALA 4.6 4.3 - - - +
500A PRO* 1.3 74.3 - - - +
502A VAL* 1.3 65.2 + - - +
503A HIS* 3.6 6.6 + - + -
568A GLN* 3.0 31.8 + - - +
569A PHE* 3.1 28.3 + - - +
570A GLY* 3.4 4.7 + - - -
632A ILE* 3.5 2.7 - - - -
633A SER* 2.8 47.7 + - - -
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Residues in contact with VAL 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ASP* 1.3 71.4 - - - +
503A HIS* 1.3 63.2 + - - +
504A LEU* 3.7 26.7 - - + +
517A VAL* 4.0 19.1 - - + -
568A GLN* 3.2 29.8 - - - +
569A PHE* 2.8 44.3 + - + +
571A LEU* 3.6 40.8 - - + -
631A TYR 4.0 5.2 - - - +
632A ILE* 4.5 7.2 - - + +
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Residues in contact with HIS 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASP* 4.9 6.1 + - - -
501A ASP* 3.6 24.2 + - - +
502A VAL* 1.3 75.6 - - - +
504A LEU* 1.3 60.0 + - - +
505A GLN* 4.8 2.0 - - - +
567A PHE 3.6 5.2 - - - -
568A GLN* 3.5 36.7 + - + +
629A PRO 4.0 2.8 - - - +
630A SER* 3.4 5.5 - - - -
631A TYR* 2.8 79.5 + + + +
633A SER* 4.3 6.8 - - - -
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Residues in contact with LEU 504 (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* 4.9 5.4 - - + -
502A VAL* 3.8 16.4 - - + -
503A HIS* 1.3 74.0 - - - +
505A GLN* 1.3 60.6 + - - +
506A ALA* 4.0 13.2 - - + -
515A TRP* 3.8 45.1 - - + -
517A VAL* 4.9 11.0 - - + -
565A LEU 3.4 1.2 - - - +
566A ALA* 3.4 4.0 - - - +
567A PHE* 2.8 48.4 + - + +
569A PHE* 5.0 1.8 - - + -
588A VAL* 4.9 10.1 - - + -
622A VAL* 3.8 24.2 - - + -
630A SER* 3.7 19.3 - - - +
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Residues in contact with GLN 505 (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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503A HIS 4.8 2.2 - - - +
504A LEU* 1.3 72.3 + - - +
506A ALA* 1.3 61.2 + - - +
564A PRO* 4.6 3.0 - - + +
565A LEU* 3.5 16.0 + - - -
566A ALA* 3.4 26.7 + - - +
622A VAL* 3.7 1.0 - - - +
623A TYR* 2.8 35.7 + - + -
628A GLN* 3.9 43.0 + - + +
629A PRO* 3.8 21.3 + - + +
630A SER* 2.9 13.9 + - - +
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Residues in contact with ALA 506 (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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504A LEU* 3.9 20.8 - - + -
505A GLN* 1.3 74.6 - - - +
507A SER* 1.3 61.4 + - - +
515A TRP* 3.8 26.9 - - + -
563A GLN 3.8 0.9 - - - +
564A PRO* 4.1 1.3 - - - -
565A LEU* 3.0 32.6 + - - +
567A PHE* 3.6 12.3 - - + -
621A ARG 3.1 14.8 - - - +
622A VAL* 4.4 3.4 - - + -
623A TYR* 4.3 1.8 - - - -
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Residues in contact with SER 507 (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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506A ALA* 1.3 74.3 - - - +
508A THR* 1.3 61.3 + - - +
515A TRP* 3.7 6.5 - - - -
562A ASN* 4.2 6.9 - - - -
563A GLN 3.3 36.6 - - - -
564A PRO* 3.7 5.1 - - - +
565A LEU* 6.1 0.2 - - - -
619A THR 3.9 0.6 + - - +
620A GLN* 3.4 3.8 - - - -
621A ARG* 2.9 52.7 + - - +
623A TYR* 3.6 8.3 + - - -
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Residues in contact with THR 508 (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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507A SER* 1.3 75.9 - - - +
509A SER* 1.3 62.0 + - - +
510A GLY* 3.2 26.8 + - - +
512A ASP 4.2 1.3 - - - +
513A SER* 3.3 16.6 + - - +
515A TRP* 4.5 2.7 - - + -
559A LEU* 3.9 33.2 - - + -
560A THR 4.2 2.5 + - - +
561A SER* 3.4 3.5 - - - -
562A ASN* 2.8 23.0 + - - -
563A GLN 4.8 0.6 + - - -
618A ALA* 3.5 4.3 - - - +
619A THR 3.5 5.8 - - - -
620A GLN* 2.6 24.6 + - - +
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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