Contacts of the strand formed by residues 693 - 699 (chain K) in PDB entry 6R1U
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 LEU 693 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683K HIS* 3.5 16.4 + - + -
690K LYS* 3.0 41.7 + - + +
691K ARG 3.2 1.7 - - - +
692K GLY* 1.3 73.3 - - - +
694K PHE* 1.3 114.9 + - + +
695K ALA 3.6 0.2 - - - -
713K ILE* 4.4 11.7 - - + -
717K ALA* 3.7 19.4 - - + +
720K SER* 5.1 5.8 - - - +
721K VAL* 5.5 5.8 - - + -
732K GLN* 3.5 26.0 - - + +
736K THR* 5.3 4.3 - - - +
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Residues in contact with PHE 694 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662K ILE* 3.7 21.8 - - + -
683K HIS* 2.9 22.6 + - - +
693K LEU* 1.3 105.6 - - + +
695K ALA* 1.3 64.6 + - - +
696K VAL 3.3 2.5 - - - -
697K PHE* 3.7 16.0 - - + -
711K SER* 3.3 26.5 - - - +
712K VAL 3.1 22.4 + - - -
713K ILE* 3.8 16.8 - - + -
729K VAL* 4.0 18.2 - - + -
732K GLN* 4.0 6.3 - - + -
733K CYS* 3.5 37.7 - - + -
736K THR* 3.9 15.5 - - + -
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Residues in contact with ALA 695 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538K PHE* 3.3 22.0 - - + -
541K SER* 3.6 29.4 - - - +
542K ASN* 5.6 2.0 - - - +
545K TYR* 6.5 0.9 - - + -
682K GLY* 3.3 0.3 - - - -
683K HIS* 2.7 36.0 + - - +
685K PRO* 6.2 0.2 - - + -
691K ARG 3.7 10.3 - - - +
692K GLY* 4.6 2.4 + - - -
693K LEU 3.6 0.8 - - - -
694K PHE* 1.3 76.0 - - - +
696K VAL* 1.3 62.5 + - + +
712K VAL* 4.1 4.2 + - - +
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Residues in contact with VAL 696 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465K CYS* 4.8 1.1 - - - -
538K PHE* 4.0 20.4 - - + -
542K ASN* 4.5 12.6 - - - +
545K TYR* 6.5 0.4 - - + -
680K PHE* 3.9 18.2 - - + -
681K PHE 3.5 11.0 - - - +
682K GLY* 4.8 1.1 - - - -
695K ALA* 1.3 89.0 - - + +
697K PHE* 1.3 63.3 + - - +
698K TYR* 3.5 39.3 - - + +
711K SER* 2.8 28.4 + - - -
712K VAL* 4.0 4.6 + - + +
7M ALA* 4.4 14.6 - - + -
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Residues in contact with PHE 697 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664K LEU* 5.2 2.5 - - + -
680K PHE* 3.1 8.0 - - - +
681K PHE* 2.9 71.1 + + + -
683K HIS* 4.8 2.5 - - + -
694K PHE* 3.7 36.3 - - + -
696K VAL* 1.3 78.3 - - - +
698K TYR* 1.3 60.3 - - - +
709K LEU* 4.3 15.0 - - + -
710K MET 3.3 6.3 - - - -
711K SER* 3.7 17.0 - - - -
733K CYS* 3.8 20.0 - - - -
736K THR* 4.2 6.5 - - + -
737K LEU* 3.6 30.7 - - + -
740K LEU* 4.0 19.3 - - + -
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Residues in contact with TYR 698 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438K ILE* 4.3 20.1 - - + +
461K PHE* 4.8 11.0 - + + -
545K TYR* 4.0 25.3 + - - -
574K LEU* 5.9 1.8 - - + -
679K ASP 3.7 3.6 - - - +
680K PHE* 3.9 30.1 - + + -
696K VAL* 3.5 35.5 - - + +
697K PHE* 1.3 75.0 - - - +
699K ASP* 1.3 62.2 + - - +
700K MET* 3.4 22.2 + - - +
709K LEU* 3.4 7.6 - - - -
710K MET* 2.7 67.7 + - + +
712K VAL* 4.3 10.8 - - + -
6M THR* 5.7 2.2 - - - -
7M ALA* 4.7 9.3 + - + +
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Residues in contact with ASP 699 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461K PHE* 5.9 1.9 - - - -
574K LEU* 4.6 7.1 - - - +
669K ARG* 2.6 43.1 + - - -
671K TRP* 3.0 23.5 + - - +
675K VAL* 6.2 0.4 - - + -
677K GLY 5.8 0.2 - - - -
678K ALA 4.2 10.9 - - - +
679K ASP* 2.9 25.6 + - - +
680K PHE* 4.7 0.8 - - - +
681K PHE* 5.8 1.9 - - + -
697K PHE 4.1 0.6 + - - -
698K TYR* 1.3 69.6 - - - +
700K MET* 1.3 65.2 + - - +
701K ASP* 3.1 22.8 + - - +
702K PRO* 4.7 2.1 - - - +
704K LYS* 4.0 10.0 + - - +
706K HIS 4.6 0.5 - - - +
708K VAL 4.2 0.7 - - - +
709K LEU* 4.0 10.0 - - + +
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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