Contacts of the strand formed by residues 921 - 934 (chain A) in PDB entry 4CAK
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 GLN 921 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A ASP 4.4 6.3 - - - +
875A PRO* 3.4 15.4 - - + +
876A VAL 2.7 32.9 + - - -
919A LEU 4.4 4.6 - - - +
920A ASP* 1.3 69.2 - - - +
922A PHE* 1.3 57.2 + - - +
923A VAL* 5.2 0.9 - - + -
955A LEU 3.6 8.1 + - - +
956A LEU* 3.4 35.4 - - - +
957A ARG* 3.3 30.6 - - - +
686B GLU* 4.4 2.7 - - + +
687B CYS 1.4 24.4 + - - +
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Residues in contact with PHE 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A LEU* 4.1 16.6 - - + -
876A VAL* 3.6 7.9 - - + -
878A VAL* 3.6 24.2 - - + -
913A SER 5.5 0.2 - - - -
914A LEU* 3.6 16.6 - - + -
916A GLN 4.3 2.5 - - - -
917A ARG* 4.0 9.2 - - + -
921A GLN* 1.3 73.2 - - - +
923A VAL* 1.3 68.0 + - - +
924A LEU* 4.2 2.2 - - + -
954A GLN* 3.5 0.9 - - - +
955A LEU* 2.8 49.6 + - + +
658B LYS* 5.0 0.4 - - - -
662B ASP* 3.2 24.0 - - + -
688B CYS* 0.9 181.0 - - + -
689B LYS 3.3 2.0 - - - -
690B GLY 3.7 4.0 - - - -
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Residues in contact with VAL 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A PRO* 4.3 23.1 - - + -
876A VAL 3.0 10.8 + - - +
877A LEU* 3.8 14.1 - - + +
878A VAL* 3.1 26.1 + - - +
921A GLN* 4.7 0.9 - - + +
922A PHE* 1.3 79.8 - - - +
924A LEU* 1.3 61.3 + - - +
925A GLN 3.5 0.7 + - - -
952A TRP* 4.3 33.9 - - + -
953A THR 3.4 10.1 - - - +
954A GLN* 4.5 10.8 - - + -
664B VAL* 4.1 6.5 - - + -
686B GLU* 4.5 1.1 - - - +
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Residues in contact with LEU 924 (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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780A VAL* 5.1 7.2 - - + -
782A HIS* 3.8 9.0 - - + +
804A PRO* 5.2 3.8 - - + -
812A LEU* 4.4 10.5 - - + -
813A LEU* 3.2 49.4 - - + -
878A VAL* 3.5 30.7 - - + -
909A LEU* 3.7 14.8 - - + -
922A PHE* 5.3 0.7 - - + -
923A VAL* 1.3 70.1 - - - +
925A GLN* 1.3 59.7 + - - +
951A VAL 3.6 1.6 - - - +
952A TRP* 3.4 4.6 - - - -
953A THR* 2.6 51.0 + - + +
955A LEU* 4.3 20.0 - - + -
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Residues in contact with GLN 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A HIS* 4.9 0.9 - - - -
804A PRO* 3.5 22.9 - - - +
877A LEU* 3.2 26.2 - - + +
878A VAL 3.0 8.1 + - - +
879A SER* 3.8 28.4 - - - -
880A CYS 4.3 2.9 + - - -
881A ASP* 5.2 2.8 + - - -
923A VAL 4.5 0.2 - - - +
924A LEU* 1.3 74.0 - - - +
926A SER* 1.3 70.8 + - - +
927A HIS* 4.5 14.3 + - - +
950A GLN* 2.8 25.8 + - - +
951A VAL 3.5 3.1 - - - -
952A TRP* 3.5 21.7 + - + +
655B CYS* 5.0 6.3 - - - +
656B THR* 3.8 19.5 + - - +
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Residues in contact with SER 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A HIS* 2.7 31.8 + - - -
784A TYR* 3.2 17.7 + - - -
802A HIS 3.5 14.6 - - - -
803A LEU* 3.9 18.2 - - - -
804A PRO* 4.7 3.1 - - - -
880A CYS* 6.1 0.4 - - - -
925A GLN* 1.3 84.5 - - - +
927A HIS* 1.3 63.1 + - - +
950A GLN* 3.5 4.5 - - - +
951A VAL* 3.1 25.2 + - - +
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Residues in contact with HIS 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A TYR* 3.7 2.7 - - - -
800A SER 4.0 0.5 - - - +
801A ILE* 3.6 2.3 - - - +
802A HIS* 2.7 49.6 + - + +
880A CYS* 6.1 2.4 - - + +
925A GLN* 4.5 13.7 + - - +
926A SER* 1.3 75.6 - - - +
928A ALA* 1.3 73.9 + - - +
929A TRP* 3.5 27.8 + + - -
948A GLU* 2.9 32.8 + - + +
949A ALA 3.6 14.6 + - - -
950A GLN* 4.4 14.8 + - + +
654B ASN 6.0 1.8 - - - -
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Residues in contact with ALA 928 (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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750A LEU* 3.8 11.5 - - + +
784A TYR* 3.6 38.6 - - + -
799A LEU* 4.4 8.1 - - + -
800A SER 3.5 7.6 - - - +
801A ILE* 4.4 4.5 - - + -
927A HIS* 1.3 81.6 - - - +
929A TRP* 1.3 59.9 + - - +
948A GLU* 3.1 7.6 - - - +
949A ALA 2.9 31.9 + - - +
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Residues in contact with TRP 929 (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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750A LEU* 4.8 0.2 - - - -
798A HIS* 5.6 0.4 + - - -
799A LEU* 3.1 6.6 - - - +
800A SER* 3.0 45.3 + - - +
802A HIS* 5.7 7.6 - + - -
927A HIS* 3.5 31.8 + + - -
928A ALA* 1.3 73.0 - - - +
930A PHE* 1.3 65.3 + - - +
946A ARG* 5.6 14.1 - - + -
947A GLY* 3.7 23.1 - - - -
948A GLU* 3.6 27.1 + - + -
606B ASP* 6.4 2.9 - - + -
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Residues in contact with PHE 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A VAL* 3.5 47.1 - - + -
750A LEU* 3.9 27.6 - - + -
786A LEU* 4.1 11.9 - - + -
797A LEU* 4.7 7.2 - - + -
798A HIS 3.4 9.9 - - - +
799A LEU* 3.8 17.5 - - + -
929A TRP* 1.3 82.1 - - - +
931A ASN* 1.3 72.6 + - - +
932A VAL* 4.7 1.3 - - + -
945A PRO* 4.1 5.4 - - + -
946A ARG* 3.4 30.3 - - - +
947A GLY* 3.1 58.2 + - - +
948A GLU 4.3 0.2 - - - -
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Residues in contact with ASN 931 (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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796A GLY 5.2 0.5 - - - +
797A LEU* 3.4 7.6 - - - +
798A HIS* 3.1 47.1 + - - +
930A PHE* 1.3 79.4 - - - +
932A VAL* 1.3 72.5 + - - +
945A PRO 3.6 11.9 - - - +
946A ARG* 4.6 5.6 - - + -
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Residues in contact with VAL 932 (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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748A VAL* 4.4 2.9 - - + -
794A VAL* 3.7 23.1 - - + -
795A ASN 3.3 15.5 - - - +
796A GLY 3.6 3.8 - - - -
797A LEU* 4.2 18.4 - - + -
930A PHE* 4.7 1.6 - - + -
931A ASN* 1.3 87.4 + - - +
933A SER* 1.3 67.5 + - - +
934A SER* 3.6 15.9 - - - +
935A LEU* 4.1 7.9 - - + -
944A LEU* 3.6 17.9 - - + +
945A PRO* 3.2 40.2 + - + +
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Residues in contact with SER 933 (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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735A ILE 5.6 0.2 + - - -
736A VAL* 4.9 15.1 - - - +
737A LEU 3.6 2.9 - - - +
738A LEU* 5.5 0.5 - - - +
795A ASN 3.5 5.8 - - - -
796A GLY* 2.9 26.4 + - - -
932A VAL* 1.3 73.8 - - - +
934A SER* 1.3 72.3 + - - +
944A LEU* 3.2 21.1 - - - +
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Residues in contact with SER 934 (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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735A ILE 4.1 10.1 - - - -
736A VAL* 3.7 7.3 - - - +
737A LEU* 2.8 37.2 + - - -
795A ASN* 2.9 33.2 + - - +
932A VAL* 3.6 1.5 - - - +
933A SER* 1.3 90.5 + - - +
935A LEU* 1.3 73.5 + - - +
944A LEU* 3.9 8.3 - - - -
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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