Contacts of the strand formed by residues 630 - 639 (chain C) in PDB entry 1DQ8
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 ARG 630 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619C LYS* 3.9 5.8 - - - +
623C ASP* 3.4 26.3 + - - +
626C SER 3.3 15.6 + - - -
627C ARG* 3.5 25.1 + - - +
628C PHE* 2.8 14.8 + - - +
629C ALA* 1.3 98.0 + - - +
631C LEU* 1.3 65.8 + - - +
632C GLN* 3.1 13.7 + - - +
649C SER* 3.0 14.3 + - - +
650C ARG* 3.9 11.5 + - + +
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Residues in contact with LEU 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C PHE* 4.1 17.5 - - + -
618C ILE* 3.4 33.9 - - + -
619C LYS* 3.0 46.2 + - + +
622C PHE* 4.0 19.9 - - + -
623C ASP* 2.8 19.4 + - - +
629C ALA 3.9 0.2 - - - -
630C ARG* 1.3 68.2 - - - +
632C GLN* 1.3 64.4 + - - +
633C LYS 3.7 15.7 - - - +
634C LEU* 4.4 1.8 - - + -
647C PHE* 3.9 16.4 - - + -
648C GLN 3.4 28.0 - - - +
649C SER* 4.0 2.6 + - - -
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Residues in contact with GLN 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586C ASP 2.6 30.2 + - - +
615C PHE* 3.7 10.2 - - - -
630C ARG 3.7 9.9 - - - +
631C LEU* 1.3 75.4 - - - +
633C LYS* 1.3 67.2 + - + +
648C GLN* 2.8 42.6 + - - +
649C SER* 3.6 2.5 - - - -
650C ARG* 2.9 41.6 - - + +
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Residues in contact with LYS 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635B HIS* 5.9 3.2 + - - -
700B GLU* 4.9 2.8 + - - -
615C PHE* 4.0 10.5 - - - -
631C LEU* 3.7 3.2 - - - +
632C GLN* 1.3 87.4 - - + +
634C LEU* 1.3 75.1 + - - +
635C HIS* 4.2 32.7 - - - +
646C ARG* 3.6 3.4 - - - +
648C GLN* 3.2 49.9 + - + +
700C GLU* 4.6 17.0 - - - +
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Residues in contact with LEU 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C LEU* 3.8 40.2 - - + +
615C PHE* 4.0 27.3 - - + -
618C ILE* 4.3 9.4 - - + -
631C LEU* 4.4 3.4 - - + -
633C LYS* 1.3 93.8 + - - +
635C HIS* 1.3 62.0 + - - +
636C THR* 4.1 9.1 + - + -
645C ILE* 3.7 21.1 - - + -
646C ARG 3.3 6.1 - - - +
647C PHE* 3.6 32.5 - - + -
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Residues in contact with HIS 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699B ILE* 3.1 27.2 + - + -
700B GLU* 3.2 25.4 + - - -
633C LYS* 4.2 19.1 - - - +
634C LEU* 1.3 75.1 - - - +
636C THR* 1.3 69.4 + - - +
637C SER* 5.0 0.4 - - - -
644C TYR 3.9 1.0 - - - +
645C ILE* 3.7 0.3 - - - -
646C ARG* 2.8 48.5 + - + +
687C TYR* 3.0 32.6 + - - -
696C ILE* 4.2 2.2 - - + +
700C GLU* 3.4 23.7 + - + +
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Residues in contact with THR 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C LYS* 2.8 47.4 + - + +
609C LEU* 4.3 29.2 - - + -
610C GLU* 3.6 8.9 + - + +
634C LEU* 4.3 8.9 + - + +
635C HIS* 1.3 89.8 + - - +
637C SER* 1.3 62.6 + - - +
643C LEU* 4.1 11.0 - - - -
644C TYR 3.3 6.5 - - - +
645C ILE* 4.3 13.2 - - + -
687C TYR* 4.4 2.5 - - - -
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Residues in contact with SER 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B TRP 5.7 0.9 + - - -
699B ILE 5.5 2.4 + - - -
606C LYS* 5.7 0.2 - - - +
635C HIS* 5.0 1.3 - - - -
636C THR* 1.3 74.0 - - - +
638C ILE* 1.3 63.0 + - - +
643C LEU* 3.7 2.9 - - - +
644C TYR* 2.8 40.0 + - - +
687C TYR* 3.0 34.5 + - - -
742D MET* 3.1 31.1 + - - +
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Residues in contact with ILE 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B LEU* 4.0 24.0 - - + +
707B VAL* 4.1 17.0 - - + -
796B THR* 3.2 19.9 - - + +
599C ALA* 5.5 0.7 - - + +
602C SER* 3.4 36.8 - - - +
606C LYS* 3.8 24.1 - - + +
637C SER* 1.3 74.6 + - - +
639C ALA* 1.3 64.3 + - - +
640C GLY 3.3 21.3 - - - +
642C ASN 3.6 4.7 - - - +
643C LEU* 3.5 23.3 - - + -
644C TYR* 5.1 0.2 - - - -
742D MET* 3.3 15.2 - - - +
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Residues in contact with ALA 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778B ILE* 4.5 5.2 - - + -
780B LEU* 3.7 19.0 - - + +
796B THR* 3.6 7.0 - - - -
637C SER 4.2 0.4 + - - -
638C ILE* 1.3 74.5 - - - +
640C GLY* 1.3 65.2 + - - +
641C ARG 3.2 0.7 + - - -
642C ASN* 3.0 23.4 + - + +
644C TYR* 3.9 14.3 - - + -
738D VAL* 3.8 28.9 - - + -
742D MET* 4.1 11.9 - - - -
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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