Contacts of the strand formed by residues 664 - 669 (chain D) in PDB entry 1FVU
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 VAL 664 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616D PHE* 4.3 8.5 - - + -
642D PHE* 5.9 2.0 - - + -
651D VAL* 6.1 1.8 - - + -
655D THR* 5.0 7.2 - - + -
658D MET* 4.9 10.3 - - - -
663D VAL* 1.3 75.1 - - - +
665D TRP* 1.3 65.6 + - - +
666D ILE* 3.8 4.6 - - + +
700D ALA* 3.0 3.9 - - - -
701D SER* 2.7 56.8 + - - +
703D PRO* 4.6 6.3 - - + -
718D ASN 3.4 5.2 - - - +
719D PHE* 3.2 37.7 - - - +
720D VAL* 3.7 17.7 - - + -
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Residues in contact with TRP 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621D MET 2.9 26.2 + - - -
623D TRP* 3.5 24.2 - + + +
626D ALA* 4.0 16.6 - - + -
639D LEU* 4.0 12.0 - - + +
640D VAL* 4.0 2.9 - - - +
663D VAL 4.4 0.4 + - - -
664D VAL* 1.3 82.1 - - - +
666D ILE* 1.3 61.7 + - - +
698D CYS* 3.6 18.8 - - + -
699D VAL 3.4 19.5 - - - -
700D ALA* 3.8 5.8 - - + -
711D ILE* 3.6 27.6 - - + -
712D PRO 3.4 21.8 - - - -
713D CYS* 3.8 16.6 - - - -
715D ARG* 3.1 25.1 - - + -
717D LYS* 3.6 28.0 - - + +
718D ASN 3.1 10.3 + - - -
719D PHE* 3.9 10.3 - - + -
720D VAL 3.9 10.2 + - - -
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Residues in contact with ILE 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C TRP* 3.8 20.0 - - + -
623D TRP* 2.9 21.5 + - - -
639D LEU* 4.0 5.6 - - - -
640D VAL* 3.7 25.8 - - + +
642D PHE* 3.8 17.5 - - + -
664D VAL* 3.8 11.4 - - + +
665D TRP* 1.3 79.4 - - - +
667D GLY* 1.3 59.2 + - - +
668D LEU* 3.0 5.2 + - + -
699D VAL* 3.1 48.0 + - + +
701D SER* 3.9 9.2 - - - -
708D TRP* 3.8 30.5 - - + +
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Residues in contact with GLY 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C GLU 4.5 0.2 - - - +
284C TRP* 3.2 17.4 - - - -
285C SER* 2.8 42.8 + - - -
623D TRP* 4.0 7.6 - - - -
639D LEU* 3.7 10.1 - - - +
640D VAL 2.8 19.6 + - - -
666D ILE* 1.3 70.2 - - - +
668D LEU* 1.3 56.6 + - - -
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Residues in contact with LEU 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C GLN* 3.9 20.2 - - - +
281C SER* 3.9 9.9 - - - +
283C GLU 3.7 19.7 - - - +
284C TRP* 3.6 33.9 - - + -
290C VAL* 3.7 20.4 - - + -
623D TRP* 3.6 6.7 + - - -
666D ILE 3.0 7.9 + - - -
667D GLY* 1.3 79.6 - - - +
669D SER* 1.3 62.2 + - - +
671D VAL* 4.2 7.2 - - + -
698D CYS* 3.5 1.7 - - - -
699D VAL* 3.0 49.1 + - + -
708D TRP* 3.9 19.5 - - + -
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Residues in contact with SER 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C SER* 4.3 0.5 + - - -
623D TRP* 3.4 31.2 - - - -
668D LEU* 1.3 74.5 - - - +
670D ASP* 1.3 68.0 + - - +
671D VAL* 3.1 7.2 + - - +
674D LYS* 2.8 39.3 + - - +
696D TYR* 4.1 8.3 + - - -
697D GLU 3.9 1.8 - - - -
698D CYS* 3.4 21.3 - - - -
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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