Contacts of the strand formed by residues 461 - 465 (chain B) in PDB entry 1MS4
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 GLY 461 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443B THR* 3.3 1.9 - - - -
444B ALA 3.0 32.7 + - - +
455B PHE* 3.5 22.5 - - - -
460B GLY* 1.3 73.0 - - - -
462B ALA* 1.3 60.4 + - - -
586B VAL 3.5 2.7 - - - -
587B GLY 3.5 14.4 - - - -
588B GLY* 4.1 1.3 - - - -
590B LYS* 3.0 11.4 - - - +
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Residues in contact with ALA 462 (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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432B TRP* 4.0 22.4 - - + -
441B ALA* 4.3 7.2 - - + -
442B SER 3.1 11.4 - - - +
443B THR* 3.9 14.1 - - + -
455B PHE* 4.2 3.4 - - + -
461B GLY* 1.3 74.8 - - - +
463B LEU* 1.3 61.9 + - - +
584B PHE 4.0 0.3 - - - +
585B TYR* 3.6 5.7 - - - +
586B VAL* 2.9 42.5 + - + +
588B GLY 4.5 0.5 + - - +
590B LYS* 3.6 5.1 - - - +
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Residues in contact with LEU 463 (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 ALA* 3.1 4.7 - - - -
442B SER* 2.8 50.1 + - - +
462B ALA* 1.3 73.6 - - - +
464B TRP* 1.3 62.8 + - - +
465B PRO* 3.4 24.6 - - + +
468B GLN* 4.0 11.2 - - - +
583B HIS* 3.7 33.2 - - + +
584B PHE 3.6 2.7 - - - -
585B TYR* 4.9 0.2 - - - +
589B TYR 4.7 1.1 - - - +
590B LYS* 3.8 17.9 - - + +
591B ARG* 3.6 38.6 - - - +
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Residues in contact with TRP 464 (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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421B GLY* 3.8 22.7 - - - -
422B PHE 4.1 0.7 - - - -
423B LEU* 3.7 36.5 - - + +
434B ASP* 4.9 0.4 - - - -
439B VAL* 2.9 26.8 + - + -
440B ASN 3.5 21.0 - - - -
441B ALA* 4.0 6.1 - - + -
462B ALA 4.2 0.8 - - - -
463B LEU* 1.3 72.9 - - - +
465B PRO* 1.3 67.5 - - + +
466B VAL* 3.8 2.4 - - - +
475B TYR* 3.6 30.6 + + - -
484B LEU* 4.0 12.1 - - + -
583B HIS* 3.3 0.7 - - - -
584B PHE* 2.8 54.7 + + + +
586B VAL* 5.2 6.7 - - + -
605B VAL* 3.9 19.3 - - + -
607B LEU* 3.7 31.6 - - + -
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Residues in contact with PRO 465 (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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439B VAL* 4.2 9.9 - - + -
440B ASN 3.5 18.8 - - - +
441B ALA* 4.6 0.2 - - - -
442B SER* 5.1 0.9 - - - +
463B LEU* 3.4 18.6 - - + +
464B TRP* 1.3 88.0 - - + +
466B VAL* 1.3 59.5 + - - +
468B GLN* 3.6 31.4 - - + +
469B GLN* 2.9 28.9 + - + +
475B TYR* 3.8 8.3 - - - -
582B SER 4.1 0.2 - - - +
583B HIS* 4.0 8.3 - - + -
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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