Contacts of the helix formed by residues 619 - 634 (chain B) in PDB entry 1MZC
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 PRO 619 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B LYS* 6.6 0.2 - - - -
617B PRO 3.5 9.8 - - - +
618B ILE* 1.3 86.9 - - + +
620B GLN* 1.3 66.1 + - - +
621B ILE* 4.4 4.5 - - + +
622B VAL* 3.1 32.4 + - + +
623B ALA* 2.9 19.6 + - - +
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Residues in contact with GLN 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B ILE 3.5 2.7 + - - -
619B PRO* 1.3 72.4 - - - +
621B ILE* 1.3 66.3 + - + +
623B ALA* 3.3 10.7 + - - +
624B THR* 3.0 44.0 + - - +
665B THR* 5.6 5.5 - - - +
667B GLU* 4.6 1.6 - - - +
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Residues in contact with ILE 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN* 6.4 0.2 - - - -
587B ARG* 4.8 5.6 - - - +
619B PRO* 3.2 4.3 - - + +
620B GLN* 1.3 80.2 - - + +
622B VAL* 1.3 66.3 + - + +
624B THR* 2.7 21.5 + - - +
625B ASP* 3.0 27.4 + - - +
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Residues in contact with VAL 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 5.5 1.1 - - + -
586B LEU* 3.4 36.6 - - + -
587B ARG* 4.3 24.0 - - - +
608B LEU* 5.5 1.3 - - + -
618B ILE* 5.4 4.7 - - + -
619B PRO* 3.1 36.7 + - + +
621B ILE* 1.3 78.3 - - + +
623B ALA* 1.3 59.4 + - - +
625B ASP* 3.2 6.9 + - - +
626B VAL* 2.9 34.5 + - + +
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Residues in contact with ALA 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B LEU* 6.4 0.7 - - - -
618B ILE* 4.3 15.2 - - + +
619B PRO 2.9 12.8 + - - +
620B GLN* 3.5 17.9 - - - +
622B VAL* 1.3 78.0 - - - +
624B THR* 1.3 56.7 + - - +
626B VAL* 3.3 2.1 + - - -
627B CYS* 3.0 33.3 + - - -
663B ILE* 3.5 33.5 - - + +
665B THR* 5.8 1.8 - - + -
667B GLU* 5.0 0.7 - - - +
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Residues in contact with THR 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B GLN* 3.0 48.1 + - - +
621B ILE* 2.7 25.5 + - - +
623B ALA* 1.3 73.8 - - - +
625B ASP* 1.3 62.7 + - - +
627B CYS* 3.3 2.9 + - - +
628B GLN* 2.9 41.3 + - - +
667B GLU* 3.2 32.0 - - - +
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Residues in contact with ASP 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN* 3.2 48.0 + - - +
87A VAL* 3.8 5.8 - - + +
587B ARG* 3.1 32.5 + - - +
621B ILE* 3.0 30.1 + - - +
622B VAL 3.2 5.8 + - - +
624B THR* 1.3 82.3 + - - +
626B VAL* 1.3 59.3 + - - +
628B GLN* 3.4 12.3 + - - +
629B PHE* 3.0 23.6 + - - +
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Residues in contact with VAL 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 4.1 22.2 - - + -
586B LEU* 4.4 15.5 - - + -
604B CYS* 4.3 11.4 - - + -
608B LEU* 4.1 19.5 - - + -
622B VAL* 2.9 28.2 + - + +
623B ALA* 3.6 8.3 - - - +
624B THR 3.3 0.2 - - - -
625B ASP* 1.3 73.4 - - - +
627B CYS* 1.3 66.9 + - - +
629B PHE* 3.2 2.8 + - - +
630B LEU* 2.9 44.9 + - + +
663B ILE* 3.9 15.5 - - + -
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Residues in contact with CYS 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B ALA 3.0 21.4 + - - -
624B THR* 3.4 11.0 - - - +
626B VAL* 1.3 77.8 - - - +
628B GLN* 1.3 63.2 + - + +
630B LEU* 3.3 1.2 + - - +
631B GLU* 3.0 18.7 + - - +
660B LEU* 4.2 7.4 - - - -
663B ILE* 3.9 12.8 - - - -
667B GLU* 4.1 17.3 - - - +
668B ALA* 3.6 40.6 - - - -
671B ILE* 3.1 28.0 - - + +
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Residues in contact with GLN 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 5.9 0.2 - - - -
84A PRO* 4.2 26.1 - - - +
85A ASN* 4.6 7.9 + - - +
624B THR* 2.9 29.8 + - - +
625B ASP* 3.7 15.5 + - - +
627B CYS* 1.3 76.2 - - + +
629B PHE* 1.3 62.2 + - - +
631B GLU* 3.2 15.1 + - - +
632B LEU* 3.2 28.3 + - + +
667B GLU* 5.8 2.6 - - - +
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Residues in contact with PHE 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.7 23.1 - - - +
85A ASN 6.0 0.2 - - - +
87A VAL* 3.4 33.9 - - + +
88A VAL* 3.8 14.4 - - + -
600B ARG* 3.4 57.0 - - + -
604B CYS* 3.9 15.3 - - - -
625B ASP 3.0 10.5 + - - +
626B VAL 3.2 2.4 + - - +
628B GLN* 1.3 77.6 - - - +
630B LEU* 1.3 68.9 + - + +
632B LEU* 3.0 21.4 + - + +
633B CYS* 3.2 37.7 + - - -
644B PRO* 3.9 9.4 - - + -
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Residues in contact with LEU 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B PRO* 4.1 32.1 - - + -
604B CYS* 4.3 5.2 - - + -
626B VAL* 2.9 34.9 + - + +
627B CYS 3.8 4.0 - - - +
629B PHE* 1.3 87.8 - - + +
631B GLU* 1.3 64.2 + - - +
633B CYS* 3.1 12.0 + - + +
634B GLN 3.1 9.7 + - - -
640B PHE* 3.2 22.7 - - + -
656B ALA* 3.9 17.5 - - + +
659B ALA* 3.9 11.7 - - + -
660B LEU* 3.7 33.9 - - + -
671B ILE* 4.7 0.7 - - + -
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Residues in contact with GLU 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627B CYS 3.0 13.2 + - - +
628B GLN* 3.4 17.8 - - - +
629B PHE 3.1 0.2 - - - -
630B LEU* 1.3 76.9 - - - +
632B LEU* 1.3 63.9 + - + +
634B GLN* 3.2 24.2 + - - +
671B ILE* 3.9 36.0 - - + +
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Residues in contact with LEU 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASN* 3.5 34.5 - - - +
82A ASP* 3.5 24.5 - - - +
83A GLY* 3.6 9.4 - - - +
628B GLN* 3.2 15.7 + - + +
629B PHE* 3.0 13.5 + - + +
631B GLU* 1.3 80.3 - - + +
633B CYS* 1.3 59.0 + - - +
634B GLN 3.3 4.1 + - - +
644B PRO* 3.5 28.4 - - + +
645B GLY 4.0 4.3 + - - -
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Residues in contact with CYS 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B PRO* 4.1 12.6 - - + -
629B PHE* 3.2 49.6 + - - -
630B LEU* 3.1 12.6 + - - +
632B LEU* 1.3 76.6 - - - +
634B GLN* 1.3 63.5 + - - +
635B SER* 3.5 0.9 + - - -
640B PHE* 4.1 6.7 - - + -
641B GLY* 2.8 39.2 + - - +
643B GLY* 3.8 29.0 - - - +
644B PRO* 4.0 0.7 - - - -
645B GLY 5.6 0.8 + - - -
646B GLN 4.8 2.9 - - - +
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Residues in contact with GLN 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B LEU 3.1 3.8 + - - +
631B GLU* 3.2 19.9 + - - +
632B LEU 4.2 3.8 - - - +
633B CYS* 1.3 77.2 - - - +
635B SER* 1.3 71.2 + - - +
636B PRO* 4.0 3.3 - - - +
639B GLY 3.5 18.4 + - - +
640B PHE* 3.5 37.0 - - + -
671B ILE* 2.8 25.2 - - - +
672B ILE* 3.6 2.0 - - - +
673B ASN* 2.9 42.0 + - + +
677B LEU* 5.8 0.8 - - - +
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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