Contacts of the strand formed by residues 674 - 681 (chain D) in PDB entry 5LS6
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 VAL 674 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644D GLU 3.3 0.9 - - - +
645D ILE* 3.5 2.7 - - - -
646D ILE* 2.8 41.5 + - + +
647D SER 4.0 3.8 - - - +
648D GLN* 3.4 39.3 - - + +
651D ALA* 3.8 25.8 - - + -
666D LEU* 4.5 10.3 - - + -
667D PHE 3.4 20.4 - - - +
668D ASN* 3.9 8.1 - - - +
669D LEU* 4.2 2.9 - - - +
673D PHE* 1.3 74.9 - - - +
675D VAL* 1.3 77.6 + - - +
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Residues in contact with VAL 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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119D ASN* 4.3 12.8 - - - +
641D TYR* 4.4 14.8 - - + +
642D CYS 4.0 4.5 - - - +
643D GLY* 3.5 32.8 - - - +
644D GLU 3.3 3.6 - - - -
645D ILE* 4.6 4.5 - - + -
666D LEU* 3.5 1.2 - - - -
667D PHE* 2.8 41.6 + - + +
669D LEU* 3.7 38.1 - - + -
674D VAL* 1.3 78.3 - - - +
676D ASP* 1.3 63.4 + - - +
677D ALA 4.1 3.1 - - - +
708D ILE* 4.1 11.0 - - + -
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Residues in contact with ASP 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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644D GLU* 2.8 33.2 + - + +
646D ILE* 3.7 18.6 - - + -
654D ARG* 2.7 35.1 + - - +
658D TYR* 3.1 17.8 + - - -
665D PHE 3.4 7.5 - - - +
666D LEU* 3.8 11.6 - - + +
675D VAL* 1.3 75.4 - - - +
677D ALA* 1.3 58.0 + - - +
678D THR* 2.8 34.0 + - - -
679D ARG 3.9 2.3 + - - -
680D LYS 3.6 2.4 - - - +
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Residues in contact with ALA 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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641D TYR* 3.5 31.6 - - + +
642D CYS 3.5 21.1 - - - +
643D GLY* 4.1 2.2 - - - -
665D PHE* 3.2 11.2 + - + +
675D VAL* 4.1 1.8 - - - +
676D ASP* 1.3 70.1 - - - +
678D THR* 1.3 54.5 + - - +
679D ARG 3.7 0.2 - - - -
680D LYS 3.5 15.4 - - - +
681D GLY* 4.3 1.3 - - - -
685D ARG* 2.5 45.3 + - + -
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Residues in contact with THR 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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111D TYR 5.7 0.2 - - - +
112D SER 5.1 0.9 - - - +
113D TRP* 3.8 5.4 - - - +
658D TYR* 3.1 34.6 - - + +
665D PHE* 3.8 20.5 + - - +
676D ASP* 2.8 20.5 + - - -
677D ALA* 1.3 74.7 - - - +
679D ARG* 1.3 69.9 + - + +
685D ARG* 2.8 25.2 + - - +
809D 74D 3.9 38.4 - - + +
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Residues in contact with ARG 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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112D SER 4.7 3.4 - - - +
113D TRP* 3.5 8.2 - - - +
114D SER* 3.3 18.0 + - - -
122D VAL* 5.7 1.6 - - - +
125D GLU* 3.8 18.8 + - - -
644D GLU* 3.4 28.6 + - - +
654D ARG* 2.9 42.4 - - - +
658D TYR* 4.4 8.2 + - - +
676D ASP 3.9 3.0 + - - -
678D THR* 1.3 88.1 - - + +
680D LYS* 1.3 67.2 + - + +
809D 74D 4.6 18.5 - - - +
236E ARG* 3.7 42.5 - - - +
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Residues in contact with LYS 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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113D TRP* 4.6 1.8 - - - -
114D SER* 3.0 27.6 - - - +
116D LEU* 3.6 17.5 - - + -
120D PHE* 3.8 27.3 - - + -
643D GLY* 3.4 18.2 - - - -
644D GLU* 3.3 39.8 + - + +
676D ASP 3.6 2.3 - - - +
677D ALA* 3.5 12.0 - - - -
678D THR 3.4 0.8 - - - -
679D ARG* 1.3 83.8 - - - +
681D GLY* 1.3 57.5 + - - +
232E VAL* 4.2 25.1 + - - +
591F TRP* 3.9 28.1 - - + -
595F LYS* 6.1 0.2 - - - +
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Residues in contact with GLY 681 (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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113D TRP* 3.4 11.0 - - - -
114D SER 3.2 3.6 + - - -
115D PRO* 3.4 7.4 - - - +
116D LEU* 2.9 32.6 + - - +
642D CYS 3.5 16.4 - - - -
677D ALA* 4.3 8.9 + - - -
680D LYS* 1.3 75.3 - - - +
682D ASN* 1.3 61.3 + - - -
685D ARG* 4.5 1.8 - - - -
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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