Contacts of the strand formed by residues 615 - 620 (chain B) 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 LYS 615 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447B LYS 4.7 2.9 + - - +
448B ILE* 4.0 20.4 - - + -
449B GLU* 6.2 2.0 - - - +
452B GLN* 4.6 10.8 + - - +
453B LEU 3.3 3.6 + - - +
454B LEU* 3.3 7.1 - - + +
455B ALA 3.0 22.2 + - - -
613B ALA* 3.5 4.4 - - - +
614B ASP* 1.3 85.2 - - + +
616B ILE* 1.3 64.7 + - - +
627B TYR* 3.7 42.1 + - + +
628B GLY* 3.6 17.5 - - - +
629B THR* 4.6 13.0 - - - +
632B GLU* 6.1 0.2 - - - -
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Residues in contact with ILE 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B LEU* 3.8 3.6 - - - -
455B ALA* 3.3 14.1 - - + +
610B LEU* 3.7 51.8 - - + +
613B ALA* 4.1 2.9 - - + +
615B LYS* 1.3 79.0 - - - +
617B LEU* 1.3 59.2 + - - +
618B ILE* 4.2 6.3 - - + -
626B PHE* 3.6 26.1 - - + +
627B TYR* 3.4 9.1 - - - -
628B GLY 2.8 40.6 + - - +
629B THR 4.2 2.0 - - - -
630B PHE* 4.2 10.8 - - - +
633B LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B ILE* 4.7 4.7 - - + -
445B ASN 5.3 2.2 - - - +
446B PHE* 3.9 25.1 - - + -
454B LEU* 3.6 13.9 - - + +
455B ALA 2.8 9.9 + - - +
456B VAL* 3.3 11.3 - - + +
457B ALA 2.9 26.7 + - - +
467B LEU* 3.8 28.3 - - + -
616B ILE* 1.3 73.2 - - - +
618B ILE* 1.3 65.9 + - - +
619B LEU* 3.8 25.6 - - + -
624B SER* 3.4 27.1 - - - +
626B PHE 3.5 8.5 - - - +
627B TYR* 4.6 11.2 - - + -
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Residues in contact with ILE 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B ALA* 3.4 31.2 - - + +
458B GLY* 4.6 0.2 - - - -
610B LEU* 4.0 15.0 - - + -
616B ILE* 4.2 8.3 - - + -
617B LEU* 1.3 75.7 - - - +
619B LEU* 1.3 64.0 + - - +
624B SER* 3.7 3.5 - - - -
625B TYR* 2.8 51.9 + - + -
626B PHE* 2.9 40.8 + - + +
633B LEU* 4.6 2.2 - - + -
644B LEU* 4.4 14.4 - - + +
645B MET* 3.9 29.6 - - + -
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Residues in contact with LEU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B LEU* 4.3 7.9 - - + -
444B ILE* 3.9 19.7 - - + -
456B VAL* 3.9 24.0 - - + -
457B ALA 2.9 10.1 + - - +
458B GLY* 3.4 20.1 - - - -
459B SER 4.2 1.4 + - - -
462B ALA* 3.6 25.3 - - + +
463B GLY 3.7 28.3 - - - +
464B LYS* 4.0 3.4 - - + +
467B LEU* 4.3 11.0 - - + -
617B LEU* 3.8 30.4 + - + -
618B ILE* 1.3 77.1 - - - +
620B HIS* 1.3 62.1 + - - +
622B GLY 4.9 1.1 - - - -
623B SER 3.3 12.6 - - - +
644B LEU 4.6 1.2 - - - +
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Residues in contact with HIS 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B SER* 4.4 15.8 + - - -
462B ALA* 4.4 1.1 - - - -
618B ILE 4.1 0.2 + - - -
619B LEU* 1.3 75.2 + - - +
621B GLU* 1.3 98.6 + - + +
622B GLY 3.2 0.4 - - - -
623B SER* 2.8 29.6 + - - +
625B TYR* 4.1 23.6 - + + -
644B LEU* 3.7 26.2 + - + +
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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