Contacts of the strand formed by residues 404 - 407 (chain B) in PDB entry 4V1M
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 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B GLU* 2.6 35.2 - - + +
217B ARG 3.5 6.9 - - - +
218B SER* 3.3 25.9 + - - +
398B ARG* 3.4 27.6 + - - +
399B ASP* 4.9 4.9 + - - +
400B HIS 3.5 16.2 - - - +
401B PHE* 3.1 30.3 + - + +
402B GLY 4.2 0.7 - - - +
403B LYS* 1.3 81.9 - - - +
405B ARG* 1.4 71.6 + - - +
406B LEU* 5.7 0.7 - - - -
631B GLY 4.3 3.1 - - - +
632B ARG* 4.8 3.6 - - - -
633B VAL* 5.3 3.3 + - - +
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Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLN 3.8 0.2 - - - +
216B GLU* 3.4 6.9 - - - +
217B ARG* 2.7 71.8 + - - +
219B ALA* 3.1 33.4 - - + +
222B ILE* 4.4 2.4 - - - +
402B GLY 3.1 26.9 + - - -
403B LYS* 4.3 0.2 - - - +
404B LYS* 1.4 79.4 + - - +
406B LEU* 1.3 63.0 + - - +
407B ASP 4.1 0.4 - - - -
627B PHE* 3.1 32.7 - - - -
629B ASP* 2.2 38.6 + - - +
630B ALA 3.6 12.6 - - - +
631B GLY 3.5 4.0 - - - -
632B ARG* 3.0 29.4 - - - +
696B GLU* 5.4 1.0 + - - -
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 4.4 9.0 - - + -
215B GLN 3.5 4.0 - - - +
216B GLU* 3.6 38.8 - - + +
401B PHE* 4.7 8.7 - - + -
404B LYS 5.7 0.7 - - - -
405B ARG* 1.3 72.8 - - - +
407B ASP* 1.3 62.2 + - - +
408B LEU* 3.3 17.2 + - + +
411B PRO* 5.3 1.9 - - - +
498B THR* 4.1 24.7 - - + +
539B LEU* 4.8 5.2 - - + -
545B ILE* 3.9 22.1 - - + +
631B GLY* 2.7 31.5 + - - +
633B VAL* 3.2 33.0 - - + -
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Residues in contact with ASP 407 (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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214B ALA* 3.5 0.3 - - - -
215B GLN* 2.7 43.8 + - + +
217B ARG* 2.4 47.7 + - - +
406B LEU* 1.3 71.6 - - - +
408B LEU* 1.3 61.2 + - - +
411B PRO* 4.6 19.8 - - + +
412B LEU* 3.4 24.0 - - + +
630B ALA 5.4 0.7 - - - +
631B GLY* 5.5 0.2 - - - -
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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