Contacts of the helix formed by residues 635 - 645 (chain A) in PDB entry 3IKM
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 635 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A LYS* 4.6 5.8 - - - +
634A LEU* 1.4 100.7 - - + +
636A THR* 1.3 64.3 + - - +
637A GLY* 2.6 12.5 + - - +
638A THR* 2.6 34.8 + - - -
639A THR* 3.4 2.1 + - - -
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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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635A PRO* 1.3 82.2 - - + +
637A GLY* 1.3 66.4 + - - +
639A THR* 2.4 25.2 + - - -
640A LEU* 3.1 22.2 - - + +
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Residues in contact with GLY 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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634A LEU 5.4 0.2 - - - -
635A PRO* 2.6 10.9 + - - +
636A THR* 1.3 89.4 - - - +
638A THR* 1.3 63.6 + - - -
639A THR 2.8 0.5 + - - -
640A LEU* 3.2 14.5 + - - +
641A GLU* 2.9 32.3 - - - +
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Residues in contact with THR 638 (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 ALA 3.3 13.9 + - - +
633A LYS 4.2 1.8 - - - +
634A LEU* 3.1 50.5 - - + -
635A PRO 2.6 8.5 + - - -
637A GLY* 1.3 68.7 - - - -
639A THR* 1.3 70.2 + - - +
641A GLU* 3.5 9.2 + - - -
642A SER* 2.6 48.9 + - - +
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Residues in contact with THR 639 (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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634A LEU* 4.7 1.4 - - - +
635A PRO 3.4 1.3 + - - -
636A THR* 2.4 34.8 + - - -
637A GLY 2.8 1.8 + - - -
638A THR* 1.3 81.7 - - - +
640A LEU* 1.3 77.1 + - + +
642A SER* 4.3 0.7 - - - -
643A ALA* 3.9 13.9 + - - +
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Residues in contact with LEU 640 (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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636A THR* 3.1 35.2 - - + +
637A GLY* 3.3 8.1 - - - +
639A THR* 1.3 84.3 - - + +
641A GLU* 1.3 60.5 + - + +
643A ALA* 3.7 5.1 - - - +
644A GLY* 3.4 14.9 + - - -
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Residues in contact with GLU 641 (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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637A GLY* 2.9 38.5 - - - +
638A THR* 3.5 4.9 + - - +
640A LEU* 1.3 75.4 - - + +
642A SER* 1.3 67.5 + - - +
643A ALA 3.1 2.0 - - - -
644A GLY* 2.9 13.5 + - - +
645A VAL 3.0 9.5 + - - -
650A ARG* 3.4 25.7 + - - +
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Residues in contact with SER 642 (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 ALA 5.3 0.7 + - - -
638A THR* 2.6 55.5 + - - +
639A THR 4.3 0.9 - - - -
641A GLU* 1.3 71.6 - - - +
643A ALA* 1.3 63.7 + - - +
645A VAL* 2.9 22.3 + - - +
650A ARG* 3.7 16.7 - - - +
657A ARG* 5.5 7.4 + - - -
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Residues in contact with ALA 643 (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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639A THR 3.9 8.4 + - - +
640A LEU* 3.7 10.3 + - - +
642A SER* 1.3 76.1 - - - +
644A GLY* 1.3 69.4 + - - +
645A VAL* 2.7 17.5 + - - +
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Residues in contact with GLY 644 (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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640A LEU 3.4 7.4 + - - -
641A GLU* 2.9 10.9 + - - -
643A ALA* 1.3 77.6 - - - +
645A VAL* 1.3 65.1 + - - +
646A VAL 2.9 7.2 + - - -
650A ARG* 5.1 0.2 - - - -
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Residues in contact with VAL 645 (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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641A GLU 3.0 5.1 + - - -
642A SER 2.9 11.6 + - - +
643A ALA* 2.7 25.5 + - - +
644A GLY* 1.3 72.9 - - - +
646A VAL* 1.3 78.5 + - - +
647A CYS 2.7 30.7 - - - +
650A ARG* 2.5 51.5 + - + +
651A ALA* 3.9 14.1 - - + +
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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