Contacts of the strand formed by residues 674 - 680 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A GLY* 1.3 71.3 - - - -
675A TRP* 1.3 58.5 + - - +
696A THR* 3.9 27.4 - - + -
697A VAL 3.7 3.8 - - - -
698A HIS* 3.7 20.6 - - + +
725A ARG* 3.2 10.4 - - - +
726A GLU* 2.7 57.5 + - + +
727A ALA 4.0 9.1 + - - -
728A GLU* 3.5 40.8 + - - +
257B THR* 4.4 12.3 + - - +
590B GLU* 4.6 12.8 + - - +
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Residues in contact with TRP 675 (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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650A GLU* 3.3 34.8 - - + -
652A ILE* 3.6 32.1 - - + -
669A ILE* 3.8 9.8 - - + +
671A GLN* 3.0 43.5 + - + -
672A PRO 4.3 0.2 - - - -
673A GLY 3.5 12.2 + - - -
674A LYS* 1.3 78.7 - - - +
676A ARG* 1.3 59.6 + - - +
696A THR* 3.3 3.0 - - - -
697A VAL* 2.8 40.5 + - + +
711A LEU* 3.9 30.3 - - + -
713A LEU* 6.0 0.7 - - + -
723A LEU* 3.5 26.0 - - + -
724A VAL 3.3 20.2 - - - -
725A ARG* 3.5 28.6 - - + +
726A GLU* 5.7 0.7 - - - -
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Residues in contact with ARG 676 (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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675A TRP* 1.3 75.1 - - - +
677A GLU* 1.3 79.8 + - - +
678A ILE* 3.5 4.4 + - - -
695A GLY* 3.2 25.9 - - - -
696A THR* 3.4 26.2 + - - +
723A LEU* 3.2 5.7 - - - -
724A VAL* 2.9 38.4 + - + +
726A GLU* 2.6 37.2 + - + +
589B LEU* 4.9 4.2 - - - +
590B GLU* 3.5 33.1 + - - +
597B HIS* 4.6 9.0 - - - -
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Residues in contact with GLU 677 (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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676A ARG* 1.3 94.5 - - + +
678A ILE* 1.3 59.3 + - - +
679A LEU 4.5 6.5 - - - +
680A ASN* 3.0 32.5 - - + +
692A GLY* 3.6 4.9 - - - -
693A ASN* 2.8 56.0 + - + +
695A GLY* 6.0 0.2 - - - -
696A THR 5.5 0.2 - - - +
721A ILE* 4.1 11.1 - - + +
722A TRP 3.2 8.5 - - - +
723A LEU* 3.3 19.9 - - + +
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Residues in contact with ILE 678 (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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609A THR* 4.1 27.9 + - + +
613A HIS* 4.1 18.4 - - - +
651A ILE* 4.0 29.6 - - + -
676A ARG* 4.0 3.1 - - - +
677A GLU* 1.3 76.4 - - - +
679A LEU* 1.3 62.7 + - - +
722A TRP* 2.8 36.4 + - + +
723A LEU* 4.2 1.3 - - - +
724A VAL* 3.5 33.4 - - + -
278B TRP* 5.8 3.5 - - - -
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Residues in contact with LEU 679 (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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555A GLY* 4.8 0.9 - - - -
602A LEU* 4.1 9.2 - - + -
605A ASP* 4.4 2.7 - - + +
606A LEU* 3.1 41.3 - - + +
609A THR* 4.3 16.2 - - + +
677A GLU* 3.6 1.9 - - - +
678A ILE* 1.3 83.8 + - - +
680A ASN* 1.3 65.5 + - - +
681A THR* 3.9 20.0 - - + -
686A TYR* 4.5 9.9 - - - +
720A THR* 4.0 4.9 - - - +
721A ILE* 3.0 6.4 - - - +
722A TRP* 2.8 69.5 + - + +
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Residues in contact with ASN 680 (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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677A GLU* 3.0 30.9 - - + +
679A LEU* 1.3 77.7 - - - +
681A THR* 1.3 60.1 + - - +
682A ASP* 2.6 48.9 + - - +
683A SER* 3.1 20.5 + - - +
686A TYR* 3.2 17.1 + - - -
691A ALA 3.0 20.8 - - - +
692A GLY* 3.9 0.7 - - - -
716A PRO* 3.9 3.6 - - - +
719A ALA* 4.7 0.6 - - - +
720A THR 3.8 4.4 + - - -
721A ILE* 3.7 15.0 - - + +
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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