Contacts of the strand formed by residues 637 - 641 (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 PHE 637 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605D SER* 3.5 35.2 - - - +
606D ILE* 3.5 32.3 - - + -
609D GLY* 5.6 1.8 - - - -
610D SER 3.3 36.8 - - - -
611D LYS* 3.9 2.0 - - + -
612D LYS* 3.2 27.7 - - - +
635D ASN 3.7 3.0 + - - -
636D GLU* 1.3 74.3 - - - +
638D ILE* 1.3 59.4 + - - +
639D SER* 3.2 24.7 - - - -
640D GLU* 3.2 25.1 - - + -
710D ILE 4.0 5.6 - - - -
711D PHE* 3.4 34.2 - + + -
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Residues in contact with ILE 638 (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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611D LYS* 3.1 2.4 - - - -
612D LYS* 2.7 34.5 + - + +
614D LEU* 3.8 29.3 - - + +
628D ILE* 3.9 12.3 - - + -
632D VAL* 4.7 13.9 - - + -
636D GLU 3.6 12.6 - - - +
637D PHE* 1.3 75.2 - - - +
639D SER* 1.3 59.9 + - - +
684D ILE* 4.1 8.1 - - + -
695D CYS* 3.4 34.8 - - + -
710D ILE* 2.7 18.6 + - + +
711D PHE* 3.9 2.2 - - - +
712D ALA* 3.8 15.9 - - + +
722D LEU* 4.0 14.8 - - + -
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Residues in contact with SER 639 (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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611D LYS* 3.2 22.3 - - - +
614D LEU* 4.2 20.2 - - - +
637D PHE* 3.2 15.8 - - - -
638D ILE* 1.3 83.3 - - - +
640D GLU* 1.3 68.0 + - - +
682D ASN* 3.4 16.8 + - - -
684D ILE* 4.2 12.8 - - - -
710D ILE* 2.9 30.6 + - - +
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Residues in contact with GLU 640 (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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117D GLN 3.5 5.0 - - - +
119D ASN* 3.6 18.0 + - - -
606D ILE* 4.0 14.9 - - + +
609D GLY* 6.3 2.2 - - - -
611D LYS* 4.8 1.0 - - + +
637D PHE* 3.2 15.5 - - + -
639D SER* 1.3 74.8 + - - +
641D TYR* 1.3 58.1 + - - +
642D CYS* 3.0 28.0 + - - +
682D ASN* 2.6 34.1 + - - +
684D ILE* 4.2 0.9 - - - -
707D ARG* 2.6 52.6 + - - +
708D ILE 3.1 20.3 + - - +
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Residues in contact with TYR 641 (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* 4.1 3.6 + - - +
639D SER 3.5 4.8 + - - -
640D GLU* 1.3 71.5 - - - +
642D CYS* 1.3 66.5 + - - +
665D PHE* 4.2 8.0 - - - +
667D PHE* 2.9 43.7 - + + -
675D VAL* 4.4 10.7 - - + +
677D ALA* 3.5 31.5 - - + +
684D ILE* 3.7 17.9 - - + -
685D ARG* 3.9 28.3 + - - +
708D ILE* 2.9 41.6 + - + +
710D ILE* 3.9 19.4 - - + +
724D PHE* 3.7 32.8 - + - -
726D TYR* 5.4 0.6 + - - -
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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