Contacts of the strand formed by residues 674 - 680 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C THR* 5.3 10.9 - - + +
590C GLU* 5.8 1.6 - - - +
673D GLY* 1.3 74.4 - - - -
675D TRP* 1.3 61.4 + - - +
696D THR* 3.2 22.2 - - + -
697D VAL 3.5 4.3 - - - -
698D HIS* 3.8 19.3 - - + +
725D ARG* 3.5 6.0 - - - +
726D GLU* 2.8 61.3 + - - +
727D ALA 3.8 19.9 + - - -
728D GLU* 3.2 30.4 + - - +
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Residues in contact with TRP 675 (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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642D VAL* 5.2 0.2 - - + -
650D GLU* 3.3 31.0 - - + -
652D ILE* 3.5 31.6 - - + -
669D ILE* 3.8 10.5 - - + +
671D GLN* 3.2 38.1 + - + -
673D GLY 3.9 12.9 - - - +
674D LYS* 1.3 78.2 - - - +
676D ARG* 1.3 60.6 + - - +
696D THR* 3.5 2.0 - - - -
697D VAL* 2.7 50.0 + - + +
711D LEU* 3.9 26.0 - - + -
713D LEU* 5.9 0.2 - - + -
723D LEU* 3.3 37.9 - - + +
724D VAL 3.2 19.5 - - - -
725D ARG* 3.8 25.1 - - + +
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Residues in contact with ARG 676 (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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586C TRP 5.5 1.0 + - - -
589C LEU* 3.8 26.5 + - - +
590C GLU* 3.3 19.6 + - - -
597C HIS* 4.9 5.2 - - - -
674D LYS 4.3 0.2 + - - -
675D TRP* 1.3 74.7 - - - +
677D GLU* 1.3 74.8 + - + +
678D ILE* 3.5 1.9 + - - -
693D ASN 6.0 0.2 - - - +
695D GLY* 3.8 13.0 - - - +
696D THR* 3.6 20.9 - - - +
697D VAL* 6.0 0.2 - - - -
723D LEU* 3.3 5.1 - - - -
724D VAL* 2.8 42.6 + - + +
726D GLU* 3.2 36.9 + - + +
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Residues in contact with GLU 677 (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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676D ARG* 1.3 87.4 - - + +
678D ILE* 1.3 62.4 + - - +
679D LEU 4.4 6.7 - - - +
680D ASN* 3.1 28.9 - - + +
692D GLY* 3.6 5.9 - - - -
693D ASN* 2.7 55.0 + - + +
695D GLY 5.5 0.2 + - - -
721D ILE* 4.1 14.2 - - + +
722D TRP 3.1 10.3 - - - +
723D LEU* 3.5 18.5 - - + +
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Residues in contact with ILE 678 (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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278C TRP* 5.9 2.3 - - - -
609D THR* 3.8 34.1 + - + +
613D HIS* 4.0 31.6 - - + +
616D MET* 5.6 0.7 - - - -
651D ILE* 4.8 10.5 - - + -
676D ARG* 3.5 2.4 + - - -
677D GLU* 1.3 75.7 - - - +
679D LEU* 1.3 61.5 + - - +
722D TRP* 2.8 37.1 + - + +
723D LEU 4.2 2.9 - - - +
724D VAL* 3.4 39.7 - - + +
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Residues in contact with LEU 679 (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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555D GLY* 4.4 7.4 - - - -
602D LEU* 4.4 10.8 - - + -
605D ASP* 4.2 8.1 - - + +
606D LEU* 3.3 32.3 - - + -
609D THR* 4.1 17.7 - - - +
677D GLU* 3.5 2.8 - - - +
678D ILE* 1.3 81.7 - - - +
680D ASN* 1.3 63.9 + - - +
681D THR* 4.5 8.7 - - + -
686D TYR* 4.7 6.1 - - - +
720D THR 4.5 2.5 - - - +
721D ILE* 3.0 6.4 - - - +
722D TRP* 2.7 84.9 + - + +
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Residues in contact with ASN 680 (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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677D GLU* 3.1 29.6 - - + +
679D LEU* 1.3 78.7 - - - +
681D THR* 1.3 58.9 + - - +
682D ASP* 2.8 26.2 - - - +
683D SER* 3.0 34.5 + - - +
686D TYR* 3.2 9.3 + - - -
691D ALA 3.0 22.3 - - - +
716D PRO* 3.8 4.1 - - - +
719D ALA* 4.4 0.6 - - - +
720D THR 3.6 3.5 + - - -
721D ILE* 3.4 19.2 - - + +
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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