Contacts of the strand formed by residues 748 - 756 (chain A) in PDB entry 6MZL
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 748 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A TYR* 3.8 23.6 - + - -
690A LEU* 3.9 19.5 - - + -
691A MET* 5.0 0.2 - - - -
692A MET* 4.3 17.7 - - + -
743A PHE* 3.9 22.6 - + + +
744A GLU* 4.2 0.7 - - - +
745A ASN* 2.9 50.3 + - - +
746A ASN 3.8 0.6 - - - -
747A LEU* 1.3 90.4 - - + +
749A ARG* 1.3 61.9 + - - +
750A ALA* 3.9 17.5 - - + -
782A VAL* 5.1 1.6 - - + -
785A GLN* 3.6 46.4 - - + +
786A CYS 3.5 10.1 - - - +
787A PRO* 4.2 4.0 - - + -
788A LEU* 4.0 6.8 - - - +
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Residues in contact with ARG 749 (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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703A TYR* 4.0 5.1 + - - -
729A PRO* 3.6 43.8 + - - +
730A PHE* 3.6 22.4 - - + -
743A PHE 3.6 3.4 - - - -
744A GLU* 2.9 40.0 + - - +
748A PHE* 1.3 75.0 - - - +
750A ALA* 1.3 63.3 + - - +
785A GLN 3.3 0.3 - - - -
786A CYS* 2.4 58.0 + - + +
788A LEU* 3.6 36.4 - - + +
942A MET* 4.5 10.1 - - - +
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Residues in contact with ALA 750 (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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730A PHE* 4.2 0.7 - - - -
742A ALA* 3.3 3.1 - - - -
743A PHE* 2.8 30.7 + - - -
748A PHE* 3.9 14.7 - - + -
749A ARG* 1.3 80.3 - - - +
751A PRO* 1.3 69.2 - - + +
752A ILE* 3.7 2.4 - - - +
782A VAL* 3.7 24.0 - - + -
783A GLY 4.0 2.7 - - - +
784A GLN 3.8 11.9 - - - +
785A GLN* 3.9 9.6 - - + -
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Residues in contact with PRO 751 (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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730A PHE* 3.6 23.3 - - + -
740A LEU* 4.1 21.3 - - + -
741A GLN 3.3 12.3 - - - +
742A ALA* 3.9 3.1 - - + -
750A ALA* 1.3 85.3 - - + +
752A ILE* 1.3 58.5 + - - +
753A TYR* 4.4 15.0 - - + +
781A VAL 3.7 1.0 - - - +
782A VAL* 3.4 1.9 - - - -
783A GLY* 2.8 40.9 + - - -
784A GLN 3.7 14.6 - - - +
786A CYS* 5.8 0.2 - - - -
1070A PHE* 5.5 4.7 - - + -
1073A GLN* 4.9 9.4 - - + +
1074A ASN* 5.4 1.8 - - - +
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Residues in contact with ILE 752 (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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700A ILE* 3.7 28.9 - - + -
741A GLN* 2.8 29.0 + - + +
742A ALA 3.5 14.1 - - - +
743A PHE* 3.6 59.0 - - + +
750A ALA 3.7 1.6 - - - +
751A PRO* 1.3 78.1 - - - +
753A TYR* 1.3 74.0 + - - +
754A LEU 4.3 0.2 - - - -
780A PHE* 3.7 24.9 - - + -
781A VAL 3.4 4.9 - - - +
782A VAL* 3.7 13.0 - - + -
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Residues in contact with TYR 753 (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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740A LEU* 3.6 23.2 - - + +
741A GLN 5.5 1.1 - - - -
751A PRO* 4.4 16.0 - - + +
752A ILE* 1.3 83.0 - - - +
754A LEU* 1.3 63.2 - - - +
755A HIS* 3.2 21.2 - - + +
780A PHE* 3.3 6.1 - - - -
781A VAL 3.0 35.8 + - - +
1073A GLN* 4.1 8.9 - - + +
1074A ASN* 2.3 43.2 + - + -
1077A LEU* 3.5 44.9 - - + +
1078A SER* 4.3 14.8 - - - -
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Residues in contact with LEU 754 (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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718A LYS* 5.2 11.7 - - + +
719A TYR* 4.8 7.2 - - + -
741A GLN* 4.2 16.0 + - - +
753A TYR* 1.3 70.8 - - - +
755A HIS* 1.3 79.2 + - - +
778A ASP* 3.9 30.5 - - + +
779A ILE 4.2 2.7 - - - +
780A PHE* 3.6 37.7 - - + -
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Residues in contact with HIS 755 (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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753A TYR* 3.2 28.8 - - + +
754A LEU* 1.3 84.9 + - - +
756A LYS* 1.3 68.0 + - - +
777A VAL 3.8 2.4 - - - +
778A ASP* 4.0 1.6 - - - +
779A ILE* 2.8 38.7 + - + +
781A VAL* 3.5 22.7 - - + +
1077A LEU 2.8 29.8 + - - -
1078A SER* 3.7 21.5 - - - -
1079A SER 4.1 4.7 - - - -
1080A THR* 4.6 11.9 - - + +
137J THR* 4.6 9.9 - - + -
138J LEU* 5.7 2.8 + - - +
139J PRO* 4.1 13.9 - - + +
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Residues in contact with LYS 756 (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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755A HIS* 1.3 79.9 - - - +
757A MET* 1.3 68.6 + - - +
758A PRO* 3.6 6.6 - - - +
777A VAL* 3.6 5.4 - - + +
778A ASP* 6.0 0.9 - - - +
779A ILE* 3.8 6.4 - - - +
137J THR* 5.5 3.3 - - - +
138J LEU* 5.7 5.2 - - - +
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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