Contacts of the strand formed by residues 664 - 674 (chain A) in PDB entry 1FCP
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 TYR 664 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY* 5.2 5.4 - - - -
646A ARG 5.3 0.9 - - - -
647A TYR* 3.4 2.4 - - - -
648A THR* 2.8 70.6 + - + +
649A GLY 5.2 0.9 - - - -
661A VAL* 5.2 0.7 - - + -
662A GLY 3.4 21.8 - - - -
663A SER* 1.3 76.8 + - - +
665A THR* 1.3 68.2 + - - +
666A VAL* 4.5 8.1 - - + -
695A ARG* 3.7 22.4 - - - +
697A TYR* 3.3 49.5 - + + -
698A VAL 3.4 21.3 - - - -
699A ALA* 3.1 25.9 + - - +
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Residues in contact with THR 665 (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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645A GLY* 5.0 4.5 - - - -
646A ARG 3.3 18.8 - - - +
647A TYR* 3.0 30.2 - - + +
664A TYR* 1.3 71.7 - - - +
666A VAL* 1.3 70.0 + - - +
667A VAL* 4.4 8.7 + - + +
693A PHE* 5.9 2.1 - - - -
695A ARG* 3.1 31.3 + - - +
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Residues in contact with VAL 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A GLY* 3.3 1.9 - - - -
646A ARG* 2.9 64.7 + - - +
664A TYR* 4.5 6.5 - - + -
665A THR* 1.3 79.2 - - - +
667A VAL* 1.3 66.7 + - - +
668A ASP* 4.2 0.7 + - - +
691A ASN* 3.3 39.5 - - + +
695A ARG* 5.1 1.6 - - + -
697A TYR* 3.6 44.0 - - + +
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Residues in contact with VAL 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A THR* 3.8 11.0 - - - +
644A GLY 3.3 13.2 - - - +
645A GLY* 4.7 5.4 - - - -
665A THR* 5.1 9.4 - - + +
666A VAL* 1.3 79.3 - - - +
668A ASP* 1.3 73.6 + - - +
691A ASN* 2.9 25.4 + - - +
692A LEU* 2.9 31.5 + - + +
693A PHE* 3.6 33.0 - - + +
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Residues in contact with ASP 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A HIS* 4.7 7.9 - - + -
72A TYR* 2.7 24.5 + - - +
626A TRP* 4.5 5.8 - - - +
643A THR* 2.8 19.7 + - - -
644A GLY 2.7 22.4 + - - +
646A ARG* 2.4 44.2 + - - +
666A VAL 4.5 0.3 - - - +
667A VAL* 1.3 77.6 - - - +
669A ALA* 1.3 62.8 + - - +
689A VAL 3.5 6.3 - - - +
690A ASN* 3.1 31.6 + - - +
691A ASN 3.8 1.4 + - - -
692A LEU* 5.4 0.2 - - - -
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Residues in contact with ALA 669 (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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626A TRP* 5.5 1.1 - - - -
642A GLY 3.4 7.9 - - - +
643A THR* 4.0 7.9 - - - +
668A ASP* 1.3 76.6 - - - +
670A LEU* 1.3 65.7 + - - +
671A VAL* 6.2 1.3 - - + -
687A LEU 4.8 0.2 - - - -
688A HIS* 3.8 3.8 + - - +
689A VAL* 3.2 40.4 + - + +
692A LEU* 4.2 22.0 - - + +
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Residues in contact with LEU 670 (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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60A LEU* 3.4 48.7 - - + +
626A TRP* 3.7 17.9 - - + -
640A THR* 4.7 11.7 - - + +
641A LEU* 3.3 4.3 - - - +
642A GLY* 2.5 42.7 + - - +
669A ALA* 1.3 78.9 - - - +
671A VAL* 1.3 94.0 + - - +
672A ARG* 4.0 13.5 - - + +
686A ALA* 4.6 0.7 - - + -
687A LEU 3.7 6.1 - - - +
688A HIS* 3.6 28.0 - - + +
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Residues in contact with VAL 671 (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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639A LEU* 5.5 2.9 - - + -
640A THR 3.3 4.7 - - - -
641A LEU* 3.6 22.4 - - + -
669A ALA* 6.2 1.3 - - + -
670A LEU* 1.3 84.3 - - - +
672A ARG* 1.3 60.6 + - - +
685A VAL 4.2 0.3 - - - +
686A ALA* 3.4 2.9 - - - +
687A LEU* 3.0 57.6 + - + +
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Residues in contact with ARG 672 (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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59A ALA* 4.3 20.0 + - - +
60A LEU* 4.8 14.9 - - - +
639A LEU* 3.3 7.5 - - - +
640A THR* 2.6 60.5 + - - +
670A LEU* 4.1 15.5 - - + -
671A VAL* 1.3 74.8 - - - +
673A TYR* 1.3 61.3 + - - +
674A ASP* 4.3 3.6 - - - +
682A GLY 5.6 2.6 + - - -
684A ASN* 3.1 46.9 + - + +
685A VAL 3.8 1.8 - - - -
686A ALA* 3.9 8.2 - - + +
688A HIS* 5.6 0.4 - - - -
720A THR* 5.8 0.4 - - - +
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Residues in contact with TYR 673 (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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635A PRO 5.4 5.5 + - - -
636A LEU* 5.6 0.7 - - - -
637A SER 3.7 19.1 - - - -
638A GLY 3.1 18.8 - - - -
639A LEU* 4.4 15.9 - - + -
672A ARG* 1.3 76.4 - - - +
674A ASP* 1.3 77.5 + - - +
675A LEU* 3.3 19.2 + - + +
677A ARG* 3.4 25.2 - - + +
678A VAL* 5.6 6.8 - - + +
684A ASN* 3.3 17.5 - - - +
685A VAL* 3.1 23.8 + - + +
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Residues in contact with ASP 674 (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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638A GLY* 2.6 31.0 + - - +
672A ARG* 4.3 3.2 - - - +
673A TYR* 1.3 90.2 - - - +
675A LEU* 1.3 59.5 + - - +
676A ALA* 2.7 45.7 + - - +
677A ARG* 4.3 6.8 + - - +
682A GLY* 4.1 11.7 + - - -
683A SER 3.8 10.5 - - - +
684A ASN* 4.3 3.1 - - - -
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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