Contacts of the strand formed by residues 672 - 677 (chain F) 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 ILE 672 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631F ASN* 2.9 29.1 + - - +
632F CYS* 4.0 14.4 - - - -
645F GLY* 3.9 9.2 - - - -
646F SER 3.7 16.4 + - - +
649F ARG* 3.4 29.4 - - - +
650F THR 3.4 23.6 - - - +
651F VAL* 3.8 15.7 - - + -
668F HIS* 5.9 2.0 - - + +
670F GLY 4.3 3.1 - - - +
671F PRO* 1.3 73.1 - - - +
673F HIS* 1.3 62.9 + - - +
674F SER 3.4 23.3 - - - +
675F LEU* 5.2 3.1 - - + -
686F THR* 5.6 3.8 - - - -
687F GLY 3.7 8.7 - - - +
688F ALA* 4.6 5.4 - - + +
60H MET* 3.8 2.9 - - - +
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Residues in contact with HIS 673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631F ASN* 5.2 0.7 - - - -
632F CYS* 5.2 6.9 - - - +
671F PRO* 3.3 17.4 + - + +
672F ILE* 1.3 74.2 - - - +
674F SER* 1.3 66.5 + - - +
687F GLY 3.5 5.6 + - - +
688F ALA 4.5 1.8 - - - -
689F THR* 3.1 44.6 + - - +
713F THR* 4.4 21.7 + - + +
714F VAL 3.3 18.8 - - - +
715F CYS* 4.2 6.9 - - - +
59H HIS* 3.6 36.7 + + + +
60H MET* 3.4 27.4 - - + +
62H LYS* 5.6 6.4 + - - -
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Residues in contact with SER 674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632F CYS* 4.3 5.6 - - - -
672F ILE* 3.4 11.8 - - - +
673F HIS* 1.3 81.0 + - - +
675F LEU* 1.3 63.4 - - - +
686F THR* 3.8 1.7 - - - -
687F GLY 3.3 25.3 + - - +
714F VAL* 2.9 15.1 + - - -
715F CYS 2.8 28.8 + - - -
717F LEU* 4.0 28.0 - - - -
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Residues in contact with LEU 675 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632F CYS* 3.7 26.1 - - + +
634F ARG* 3.4 29.8 - - + +
643F ALA* 3.7 15.5 - - + -
645F GLY* 4.9 3.6 - - - +
651F VAL* 3.8 34.5 - - + -
672F ILE* 5.4 1.1 - - + -
674F SER* 1.3 78.0 - - - +
676F THR* 1.3 75.4 + - - +
677F PHE* 3.7 31.0 - - + -
684F LEU* 4.6 2.5 - - + -
685F ALA 3.4 7.4 - - - +
686F THR* 3.8 21.5 - - + -
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Residues in contact with THR 676 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634F ARG* 3.5 14.6 - - - +
675F LEU* 1.3 83.5 - - - +
677F PHE* 1.3 80.2 + - - +
684F LEU* 3.5 2.1 - - - +
685F ALA* 2.9 46.3 + - - +
717F LEU* 3.3 37.3 - - + +
718F ARG* 4.0 14.1 - - - +
719F PHE* 4.2 12.4 + - - -
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Residues in contact with PHE 677 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634F ARG* 3.5 15.0 + - + +
635F PHE 3.2 28.9 - - - +
636F HIS* 3.3 37.9 - + + +
637F PRO* 4.5 7.4 - - + -
641F TYR* 4.7 2.7 - - + -
642F VAL 4.8 0.9 - - - -
643F ALA* 3.6 24.9 - - + -
653F LEU* 4.2 10.8 - - + -
675F LEU* 3.7 12.3 - - + -
676F THR* 1.3 87.8 - - - +
678F SER* 1.3 64.9 - - - +
679F PRO* 4.5 0.3 - - - +
683F PHE 3.4 5.8 - - - +
684F LEU* 3.6 36.6 - - + -
698F ILE* 6.0 2.5 - - + -
718F ARG* 5.7 2.3 + - - -
719F PHE* 3.2 24.9 - - - +
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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