Contacts of the helix formed by residues 606 - 615 (chain S) in PDB entry 1I84
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 ASN 606 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401S SER 2.5 31.6 + - - -
402S ILE* 4.3 3.7 - - + +
405S PRO* 4.4 11.1 - - - +
418S GLN* 4.7 7.5 + - - +
426S ALA* 4.4 20.2 - - + +
605S LEU* 1.4 74.5 - - + +
607S ASP* 1.3 62.7 + - - +
608S ASN* 2.7 12.5 + - - +
609S VAL* 2.4 50.6 + - + +
610S THR* 3.0 7.9 + - - -
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Residues in contact with ASP 607 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407S ILE* 5.5 9.4 - - - +
408S LYS 5.8 0.5 + - - -
605S LEU 2.8 3.8 + - - +
606S ASN* 1.3 67.8 - - - +
608S ASN* 1.3 67.1 + - - +
609S VAL 3.2 0.2 - - - -
610S THR* 3.2 13.9 - - + -
611S SER* 2.6 36.9 + - - +
628S VAL* 5.9 0.2 - - + -
631S ILE* 3.7 17.9 - - + -
632S VAL 2.8 16.7 - - - +
633S GLY* 3.1 28.7 - - - +
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Residues in contact with ASN 608 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400S ARG* 5.1 5.1 - - - +
401S SER* 3.4 30.1 + - - +
405S PRO* 4.0 4.4 - - - +
406S ARG* 3.4 43.2 + - - +
407S ILE* 3.6 16.8 + - - +
606S ASN* 2.7 17.8 + - - +
607S ASP* 1.3 85.7 - - - +
609S VAL* 1.3 57.1 - - - +
611S SER* 4.0 3.0 + - - -
612S LEU* 3.2 19.1 + - - +
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Residues in contact with VAL 609 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391S MET* 4.9 0.9 - - + -
393S ILE* 4.9 0.2 - - + -
398S PHE* 3.3 39.0 - - + -
401S SER* 4.3 5.8 - - - -
402S ILE* 3.7 16.6 - - + -
430S LEU* 4.3 22.0 - - + -
605S LEU* 5.6 0.4 - - + -
606S ASN* 2.4 48.7 + - + +
608S ASN* 1.3 72.8 - - - +
610S THR* 1.3 70.2 + - - +
612S LEU* 2.9 27.7 - - + +
613S LEU* 3.1 20.0 - - + +
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Residues in contact with THR 610 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430S LEU* 5.7 0.9 - - - -
605S LEU* 4.4 11.3 - - - +
606S ASN 3.0 11.8 + - - -
607S ASP* 2.9 17.9 + - + +
609S VAL* 1.3 83.2 - - - +
611S SER* 1.3 69.5 + - - +
613S LEU* 2.9 25.5 + - - +
614S ASN* 3.1 8.0 + - - +
625S TRP* 4.7 5.8 - - - -
628S VAL* 2.9 47.1 - - + +
631S ILE* 3.2 28.1 - - + +
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Residues in contact with SER 611 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607S ASP* 2.6 20.0 + - - +
608S ASN* 4.0 3.1 + - - -
610S THR* 1.3 78.5 - - - +
612S LEU* 1.3 59.5 + - - +
614S ASN* 2.8 23.2 + - - +
615S GLN* 2.4 33.8 + - - -
628S VAL* 4.7 5.6 - - - +
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Residues in contact with LEU 612 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393S ILE* 3.3 45.2 - - + +
394S ASN* 4.8 1.6 - - + +
397S ASP* 3.4 32.5 - - + -
398S PHE* 3.9 11.7 - - + +
400S ARG* 6.1 0.2 - - - +
401S SER* 4.2 8.7 - - - +
608S ASN 3.2 16.5 + - - +
609S VAL* 2.9 31.2 + - + +
611S SER* 1.3 80.7 - - - +
613S LEU* 1.3 58.7 + - - +
615S GLN* 3.9 7.4 + - - +
616S SER* 3.8 9.9 + - - -
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Residues in contact with LEU 613 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391S MET* 3.3 48.2 - - + -
393S ILE* 3.7 20.4 - - + -
430S LEU* 4.7 3.8 - - + -
609S VAL* 3.1 27.8 - - + +
610S THR* 2.9 16.1 + - - +
612S LEU* 1.3 74.3 - - - +
614S ASN* 1.3 53.3 + - - +
615S GLN 2.3 21.4 + - - -
616S SER* 2.3 21.6 + - - -
621S VAL* 4.3 4.9 - - + +
622S ALA* 4.8 5.7 - - - -
625S TRP* 3.8 47.6 - - + +
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Residues in contact with ASN 614 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610S THR 3.1 4.4 + - - +
611S SER* 2.8 28.8 + - - +
613S LEU* 1.3 75.5 - - - +
615S GLN* 1.3 66.5 + - - +
622S ALA* 4.6 12.0 - - - +
625S TRP* 3.4 31.9 + - - +
626S LYS* 3.4 21.9 + - - +
628S VAL* 3.8 17.3 - - + +
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Residues in contact with GLN 615 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611S SER* 2.4 41.1 + - - +
612S LEU* 3.9 9.2 + - - +
613S LEU 2.3 14.3 + - - -
614S ASN* 1.3 85.9 - - - +
616S SER* 1.3 66.8 + - - +
617S SER* 3.7 0.5 + - - -
622S ALA* 5.7 1.3 - - - -
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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