Contacts of the strand formed by residues 674 - 680 (chain C) in PDB entry 1M7X
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 674 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673C GLY* 1.3 68.6 - - - -
675C TRP* 1.3 60.5 + - - +
696C THR* 3.4 21.1 - - + -
697C VAL 3.9 4.7 - - - -
698C HIS* 3.9 19.5 - - + +
725C ARG* 3.3 3.0 - - - +
726C GLU* 2.6 66.0 + - + +
727C ALA 3.0 22.2 + - - -
728C GLU* 3.1 38.4 + - - +
257D THR* 4.4 4.8 + - - +
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Residues in contact with TRP 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650C GLU* 3.0 34.8 - - + -
652C ILE* 3.5 37.0 - - + -
669C ILE* 3.8 12.3 - - + +
671C GLN* 2.9 46.7 + - + -
673C GLY 3.4 16.6 + - - +
674C LYS* 1.3 73.7 - - - +
676C ARG* 1.3 60.5 + - - +
696C THR* 3.9 1.2 - - - +
697C VAL* 2.9 45.4 + - - +
699C SER* 4.6 0.2 - - - -
711C LEU* 3.9 25.8 - - + -
723C LEU* 3.5 29.3 - - + +
724C VAL 3.5 3.4 - - - -
725C ARG* 3.5 34.8 - - + +
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Residues in contact with ARG 676 (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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674C LYS 4.0 0.4 + - - -
675C TRP* 1.3 74.6 - - - +
677C GLU* 1.3 77.3 + - + +
678C ILE* 5.7 1.3 - - - -
695C GLY* 3.6 28.5 - - - +
696C THR* 3.0 25.4 + - - +
723C LEU* 3.3 4.9 - - - -
724C VAL* 2.8 43.8 + - + +
726C GLU* 2.7 38.9 + - + -
586D TRP 5.8 0.2 + - - -
589D LEU* 3.4 30.0 + - - +
590D GLU* 3.8 15.6 - - - +
597D HIS* 4.8 5.8 - - - -
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Residues in contact with GLU 677 (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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676C ARG* 1.3 91.9 - - + +
678C ILE* 1.3 61.2 + - - +
679C LEU 3.5 6.5 - - - +
680C ASN* 3.3 24.6 - - + +
692C GLY* 3.7 4.3 - - - -
693C ASN* 2.8 54.9 + - + +
695C GLY 5.2 2.2 + - - -
721C ILE* 3.8 19.8 - - + +
722C TRP 3.0 9.6 - - - +
723C LEU* 3.4 19.0 - - + +
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Residues in contact with ILE 678 (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 THR* 3.9 22.1 + - + +
613C HIS* 3.3 41.3 - - + +
616C MET* 6.2 0.2 - - - -
651C ILE* 4.7 11.0 - - + -
676C ARG* 5.6 1.8 - - + -
677C GLU* 1.3 76.8 - - - +
679C LEU* 1.3 63.9 + - - +
722C TRP* 2.8 32.0 + - + +
723C LEU 4.5 0.2 - - - +
724C VAL* 3.3 42.2 - - + +
278D TRP* 6.0 1.7 - - - -
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Residues in contact with LEU 679 (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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555C GLY* 4.8 1.8 - - - -
602C LEU* 4.9 2.0 - - + -
605C ASP* 4.6 3.8 - - + -
606C LEU* 3.3 51.1 - - + +
609C THR* 4.0 13.0 - - - +
677C GLU* 3.5 3.3 - - - +
678C ILE* 1.3 81.1 - - - +
680C ASN* 1.3 62.3 + - - +
681C THR* 3.9 18.4 - - - +
686C TYR* 5.2 6.7 - - - +
720C THR 4.2 2.2 - - - +
721C ILE* 3.1 7.6 - - - +
722C TRP* 2.8 75.7 + - + +
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Residues in contact with ASN 680 (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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677C GLU* 3.3 23.8 - - + +
679C LEU* 1.3 77.6 - - - +
681C THR* 1.3 59.6 + - - +
682C ASP* 2.7 40.4 - - - +
683C SER* 3.1 28.2 + - - +
686C TYR* 3.1 18.7 + - - -
691C ALA 2.6 23.6 - - - +
692C GLY* 3.6 5.7 - - - -
716C PRO* 3.8 3.0 - - - +
719C ALA* 4.6 0.6 - - - +
721C ILE* 3.7 18.8 - - + +
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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