Contacts of the helix formed by residues 625 - 637 (chain A) in PDB entry 3CMM
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 THR 625 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A PHE* 4.6 6.4 - - - -
621A GLN* 3.1 29.6 + - + +
623A TYR 3.8 0.2 - - - -
624A PHE* 1.3 79.6 - - - +
626A ASP* 1.3 73.1 + - - +
627A SER 3.4 0.9 - - - -
628A ALA* 3.4 4.7 + - - +
629A GLU* 3.1 45.3 + - + +
818A PRO* 4.1 4.0 - - + +
819A VAL* 2.9 29.3 + - - +
821A PHE* 5.3 0.9 + - - +
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Residues in contact with ASP 626 (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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621A GLN* 2.8 38.7 + - - +
622A GLY* 4.2 7.5 + - - +
625A THR* 1.3 76.9 - - - +
627A SER* 1.3 56.7 + - - +
629A GLU* 3.5 18.7 - - - +
630A ASN* 2.8 49.6 + - - +
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Residues in contact with SER 627 (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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622A GLY 2.7 20.0 + - - -
623A TYR* 3.3 22.6 + - - -
626A ASP* 1.3 77.5 - - - +
628A ALA* 1.3 62.7 + - - -
630A ASN* 3.5 5.3 + - - +
631A VAL* 3.1 30.5 + - - +
657A SER* 4.3 18.9 + - - +
661A SER* 3.8 18.6 + - - -
741A ASN* 5.7 0.7 - - - -
816A LEU* 4.9 1.8 - - - -
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Residues in contact with ALA 628 (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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623A TYR 5.1 0.2 + - - -
624A PHE 4.5 1.3 - - - +
625A THR* 3.4 4.8 + - - +
626A ASP 3.4 0.2 - - - -
627A SER* 1.3 75.4 - - - +
629A GLU* 1.3 66.1 + - - +
631A VAL* 3.3 2.3 + - - +
632A ASN* 3.0 30.1 + - - +
741A ASN* 4.4 11.2 - - - +
816A LEU* 3.7 32.1 - - + +
817A GLU 4.2 1.3 - - - -
818A PRO* 3.8 31.9 - - + -
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Residues in contact with GLU 629 (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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625A THR* 3.1 28.6 + - - +
626A ASP* 3.5 24.2 - - - +
628A ALA* 1.3 79.7 - - - +
630A ASN* 1.3 57.2 + - - +
632A ASN* 3.3 6.3 + - - +
633A MET* 2.9 45.2 + - + +
818A PRO* 4.3 15.2 - - + +
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Residues in contact with ASN 630 (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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626A ASP* 2.8 40.4 + - - +
627A SER* 3.8 3.8 - - - +
629A GLU* 1.3 75.7 - - - +
631A VAL* 1.3 54.0 + - - +
633A MET* 3.3 22.9 + - - +
634A TYR* 2.8 34.1 + - - +
640A PHE* 4.1 6.9 - - + -
654A VAL* 4.6 20.9 - - - +
657A SER* 4.5 13.3 + - - -
658A ILE* 3.8 23.4 - - + +
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Residues in contact with VAL 631 (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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627A SER 3.1 17.5 + - - +
628A ALA 3.6 4.0 - - - +
630A ASN* 1.3 75.9 - - - +
632A ASN* 1.3 59.9 + - - +
634A TYR* 3.2 7.7 + - - +
635A LEU* 2.7 45.7 + - + +
657A SER 4.1 5.6 - - - +
658A ILE* 4.1 13.5 - - + -
661A SER* 3.7 27.1 - - - -
662A LEU* 3.8 28.0 - - + -
814A PHE* 5.4 0.9 - - + -
816A LEU* 3.8 18.2 - - + +
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Residues in contact with ASN 632 (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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628A ALA 3.0 18.5 + - - +
629A GLU* 3.8 5.5 - - - +
631A VAL* 1.3 77.0 - - - +
633A MET* 1.3 57.1 + - + +
635A LEU* 4.4 5.2 - - - +
636A THR* 2.5 40.4 + - + +
814A PHE 4.7 0.9 - - - +
815A LYS* 3.8 27.6 - - + +
816A LEU* 2.7 47.4 + - - +
818A PRO* 4.5 7.1 - - - +
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Residues in contact with MET 633 (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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629A GLU* 2.9 31.1 + - + +
630A ASN* 3.4 30.3 - - - +
632A ASN* 1.3 74.5 - - - +
634A TYR* 1.3 64.4 + - - +
636A THR* 3.9 4.3 - - - -
637A GLN* 3.0 52.9 + - - +
640A PHE* 3.7 21.8 - - + +
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Residues in contact with TYR 634 (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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630A ASN 2.8 20.2 + - - +
631A VAL 3.4 4.5 - - - +
633A MET* 1.3 75.5 - - - +
635A LEU* 1.3 71.4 + - + +
637A GLN 3.6 12.1 - - - +
640A PHE* 3.7 26.6 - + + +
641A VAL* 4.3 18.8 - - + -
655A LEU* 6.5 0.2 - - + -
658A ILE* 3.6 28.7 - - + -
662A LEU* 4.1 21.5 - - + -
805A LEU* 3.3 39.5 + - + +
806A PRO* 4.9 2.9 - - + -
807A ASP* 3.7 17.9 + - - -
808A PRO* 4.0 30.8 - - + +
811A LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 635 (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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631A VAL* 2.7 38.7 + - + +
632A ASN* 4.2 6.5 - - - +
634A TYR* 1.3 86.5 - - + +
636A THR* 1.3 63.9 + - + +
637A GLN 5.0 0.3 - - - +
662A LEU* 5.0 1.1 - - + -
808A PRO* 3.8 40.2 - - + +
811A LEU* 3.7 39.0 - - + +
812A ALA* 5.9 0.2 - - - -
814A PHE* 3.1 37.9 - - + +
815A LYS* 6.5 0.2 - - + -
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Residues in contact with THR 636 (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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632A ASN* 2.5 25.3 + - + +
633A MET* 3.6 4.7 + - - -
635A LEU* 1.3 83.3 - - + +
637A GLN* 1.3 69.6 + - - +
638A PRO* 3.8 5.4 - - - +
815A LYS* 4.7 19.5 - - + -
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Residues in contact with GLN 637 (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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633A MET* 3.0 33.7 + - - +
634A TYR 3.6 13.9 - - - +
635A LEU 5.0 0.2 - - - -
636A THR* 1.3 82.9 + - - +
638A PRO* 1.4 74.5 - - + +
639A ASN 3.6 1.0 + - - +
640A PHE* 3.4 39.7 + - + +
643A GLN* 5.6 2.8 - - - +
808A PRO* 5.9 1.2 - - - +
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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