Contacts of the strand formed by residues 654 - 658 (chain A) in PDB entry 4FOV
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 SER 654 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A PRO* 4.2 6.9 - - - +
493A GLY* 5.9 0.9 - - - -
592A GLN* 2.8 28.2 + - - +
594A SER* 2.9 25.5 + - - -
611A SER* 2.7 38.7 + - - -
612A THR* 4.8 0.2 - - - -
651A TYR* 3.6 18.0 - - - -
652A ALA 3.5 1.8 + - - -
653A TYR* 1.3 76.1 - - - +
655A ALA* 1.3 61.3 + - - +
666A VAL* 5.0 0.2 - - - -
667A LEU 3.6 5.8 - - - -
668A PHE* 3.9 6.3 - - - -
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Residues in contact with ALA 655 (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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247A PRO 3.7 5.4 - - - +
248A THR* 3.6 15.7 - - - +
249A LEU* 3.5 36.4 - - + +
493A GLY* 6.1 1.6 - - - -
594A SER* 3.9 2.9 - - - -
654A SER* 1.3 76.1 - - - +
656A ILE* 1.3 64.7 + - - +
666A VAL* 3.3 6.1 - - - +
667A LEU* 2.8 38.0 + - + +
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Residues in contact with ILE 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 4.3 2.9 - - - +
494A GLN* 3.2 21.3 + - - -
594A SER* 3.6 27.2 + - - +
595A ALA* 3.8 5.8 - - - +
596A ILE* 3.5 22.6 - - + +
609A ILE* 3.3 33.4 - - + +
610A LEU 4.4 0.7 - - - -
611A SER* 3.6 24.7 - - - +
624A LEU* 4.2 5.4 - - + -
655A ALA* 1.3 80.3 - - - +
657A THR* 1.3 60.9 - - - +
664A ILE* 4.7 8.1 - - + -
665A GLY 3.2 5.2 - - - +
666A VAL* 3.9 23.6 - - + -
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Residues in contact with THR 657 (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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249A LEU* 3.9 28.5 - - + -
250A TYR 3.9 0.2 - - - -
251A THR* 2.7 30.7 + - - +
257A VAL* 4.0 8.7 - - + -
494A GLN* 4.2 3.1 - - - -
596A ILE* 4.1 9.9 - - - -
656A ILE* 1.3 77.5 - - - +
658A GLU* 1.3 59.6 + - - +
659A LEU* 3.9 18.8 - - + -
664A ILE* 3.5 4.7 - - - +
665A GLY 2.9 34.4 + - - +
702A DMS 2.9 19.6 + - - -
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Residues in contact with GLU 658 (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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251A THR* 2.8 25.5 + - - +
596A ILE* 3.8 14.7 - - + +
597A LYS 3.9 4.2 - - - +
598A TYR* 3.2 32.0 - - + -
599A SER* 2.6 50.8 + - - -
657A THR* 1.3 72.7 + - - +
659A LEU* 1.3 74.7 + - - +
662A HIS* 2.8 20.2 + - - -
663A HIS 3.6 6.7 - - - +
664A ILE* 4.3 2.9 - - - -
702A DMS 5.1 1.2 + - - +
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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