Contacts of the strand formed by residues 599 - 603 (chain A) in PDB entry 1XMI
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 THR 599 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A THR* 2.9 15.0 + - - -
390A THR 2.5 30.8 + - - +
392A VAL* 4.2 1.3 - - + -
448A ILE* 4.0 23.8 - - + -
449A GLU 4.1 4.3 - - - +
450A ARG* 3.4 0.9 - - - -
451A GLY* 2.8 20.6 + - - +
452A GLN 3.5 12.1 - - - +
567A ASP 3.8 4.9 - - - -
568A LEU* 3.6 20.2 - - + -
569A TYR* 3.1 23.9 + - - -
598A LYS* 1.3 71.7 - - - +
600A ARG* 1.3 62.7 + - - +
601A ILE* 5.7 0.2 - - + -
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Residues in contact with ARG 600 (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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448A ILE* 5.4 0.3 - - - +
451A GLY 2.9 21.2 + - - -
452A GLN 3.0 13.1 + - - +
453A LEU* 3.7 33.8 - - + +
454A LEU* 2.9 25.6 + - - +
568A LEU* 4.6 0.7 - - - -
569A TYR* 3.3 15.0 - - + +
571A LEU* 4.0 13.9 - - + -
591A VAL* 2.8 35.0 + - + +
592A CYS* 4.3 7.5 + - - +
595A MET* 3.5 27.1 + - - -
596A ALA* 3.4 17.2 + - - +
598A LYS 2.9 23.6 + - - -
599A THR* 1.3 75.5 - - - +
601A ILE* 1.3 66.5 + - - +
602A LEU 4.1 0.2 - - - -
614A ASP* 5.2 2.0 + - - -
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Residues in contact with ILE 601 (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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392A VAL* 4.6 14.4 - - + -
446A PHE* 4.8 2.9 - - + -
448A ILE* 5.3 4.7 - - + -
454A LEU* 3.3 26.0 - - + +
456A VAL* 3.7 28.7 - - + -
467A LEU* 5.3 1.6 - - + -
468A LEU* 3.9 18.5 - - + +
471A ILE* 3.7 28.5 - - + -
568A LEU* 4.5 12.1 - - + -
569A TYR 2.9 9.1 + - - -
570A LEU* 3.6 17.7 - - + -
571A LEU* 2.8 34.5 + - - +
600A ARG* 1.3 77.2 - - - +
602A LEU* 1.3 59.3 + - - +
603A VAL 4.1 0.2 + - - -
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Residues in contact with LEU 602 (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 LEU* 4.0 19.7 - - + -
454A LEU 2.8 9.8 + - - +
455A ALA* 3.3 6.5 - - + -
456A VAL 2.8 25.4 + - - -
571A LEU* 3.4 27.8 - - + +
574A PRO* 3.7 25.4 - - + -
575A PHE* 4.2 8.5 - - + -
587A PHE* 3.7 34.1 - - + -
591A VAL* 4.6 5.6 - - + -
600A ARG 4.1 0.4 - - - -
601A ILE* 1.3 74.2 - - - +
603A VAL* 1.3 69.3 + - - +
604A THR* 3.6 11.9 + - + +
609A HIS* 4.1 16.4 - - + +
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Residues in contact with VAL 603 (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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2A ATP 5.8 0.7 - - - +
456A VAL* 3.4 11.4 - - + -
464A LYS* 3.7 49.1 - - + +
468A LEU* 3.9 31.9 - - + -
493A GLN* 6.1 0.7 - - - +
571A LEU 2.8 9.1 + - - +
572A ASP* 3.6 27.1 - - - +
573A SER* 3.1 33.4 + - - +
574A PRO* 4.4 0.2 - - - +
602A LEU* 1.3 77.1 - - - +
604A THR* 1.3 63.6 + - - +
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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