Contacts of the helix formed by residues 694 - 699 (chain C) in PDB entry 1IW1
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 SER 694 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B LEU* 4.8 2.8 + - - +
354B THR* 4.4 7.4 - - - -
355B ALA* 3.9 10.0 + - - +
358B GLN* 3.9 19.3 - - - -
410B VAL* 3.9 12.5 - - - +
414B GLU* 2.7 24.9 + - - -
417B ARG* 4.6 1.2 - - - +
688C ASP* 3.6 2.9 - - - -
693C SER* 1.3 69.2 - - - +
695C GLU* 1.3 58.0 + - - +
696C TRP* 3.0 12.2 + - - -
697C ARG* 3.2 46.0 + - - +
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Residues in contact with GLU 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 6.5 0.2 - - - -
407B ILE* 5.4 9.1 - - - +
410B VAL* 3.9 22.3 - - + +
411B ASN* 2.9 27.1 - - - +
414B GLU* 3.4 10.6 - - - +
693C SER* 3.0 22.0 + - - +
694C SER* 1.3 72.9 - - - +
696C TRP* 1.3 65.0 + - - +
697C ARG* 3.0 2.2 - - - -
698C SER* 2.9 27.8 + - - +
699C ARG* 3.8 4.2 + - - +
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Residues in contact with TRP 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647C GLU* 3.9 12.3 - - - +
650C TRP* 3.6 45.3 - + - -
684C ALA* 3.8 8.7 - - + -
687C LEU* 3.5 34.8 - - + -
688C ASP* 2.9 25.3 + - - +
691C ASN* 3.6 35.5 - - + +
693C SER* 3.2 23.4 + - - -
694C SER 3.7 1.3 - - - -
695C GLU* 1.3 77.4 - - - +
697C ARG* 1.3 102.1 + - + +
699C ARG* 2.9 19.7 + - + +
700C ILE* 3.0 29.9 + - + +
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Residues in contact with ARG 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B TRP* 3.5 36.3 - - + -
351B LEU* 3.8 21.8 - - + +
354B THR* 3.4 29.7 - - - +
358B GLN* 4.1 0.6 + - - -
397B ARG 4.2 5.5 - - - +
400B ILE* 3.9 11.3 - - - +
650C TRP* 5.0 1.8 - - + -
681C GLU* 5.8 0.2 + - - -
684C ALA* 3.6 27.1 - - - +
688C ASP* 2.8 32.9 + - - -
694C SER* 3.2 30.0 + - - +
695C GLU 3.0 1.0 - - - -
696C TRP* 1.3 104.9 - - + +
698C SER* 1.3 59.4 + - - +
699C ARG 3.6 0.5 + - - -
700C ILE* 3.7 14.9 - - - +
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Residues in contact with SER 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 3.7 12.8 - - - +
400B ILE 3.7 11.0 - - - +
401B THR* 2.8 34.7 + - - +
402B ALA* 3.0 30.9 + - - +
695C GLU* 2.9 18.7 + - - +
697C ARG* 1.3 78.6 - - - +
699C ARG* 1.3 56.0 + - - +
700C ILE 5.4 0.2 - - - -
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Residues in contact with ARG 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647C GLU* 6.1 1.8 - - - +
695C GLU 4.5 5.8 - - - +
696C TRP* 2.9 10.8 + - + +
698C SER* 1.3 79.6 - - - +
700C ILE* 1.3 67.3 + - - +
701C THR* 3.5 7.3 + - - +
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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