Contacts of the helix formed by residues 696 - 702 (chain B) in PDB entry 1Q99
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 ASP 696 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B ASP* 4.5 1.8 - - - +
694B ARG 3.7 1.6 + - - -
695B ALA* 1.3 75.0 - - - +
697B ALA* 1.3 63.6 + - - +
698B GLY* 3.6 5.4 + - - +
699B GLY* 3.5 15.2 + - - -
700B LEU* 3.2 25.2 + - - +
720B ARG* 2.6 47.3 + - - -
721B GLU 4.9 0.2 - - - +
724B GLY* 3.3 14.9 + - - +
725B SER 3.7 1.0 - - - +
726B GLY* 3.8 6.9 - - - +
729B ILE* 3.9 8.2 - - + +
732B TRP* 3.3 27.6 - - + -
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Residues in contact with ALA 697 (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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278B LEU* 3.2 47.9 - - + +
281B LEU* 3.9 10.3 - - + -
282B ASP* 3.8 13.2 - - - +
285B HIS* 5.4 1.5 - - + -
587B ILE* 3.7 15.1 - - + +
696B ASP* 1.3 71.3 - - - +
698B GLY* 1.3 67.0 + - - +
700B LEU* 3.1 6.3 + - - +
701B VAL* 3.0 24.3 + - - +
732B TRP* 4.4 0.6 - - - -
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Residues in contact with GLY 698 (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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282B ASP* 3.4 33.3 + - - +
696B ASP* 3.4 7.0 + - - +
697B ALA* 1.3 77.7 - - - +
699B GLY* 1.3 63.3 + - - +
701B VAL* 3.1 12.1 + - - +
702B ASN* 3.8 1.7 + - - -
717B VAL* 3.4 27.8 - - - +
720B ARG* 3.8 7.0 - - - -
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Residues in contact with GLY 699 (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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696B ASP* 3.5 13.4 + - - -
697B ALA 3.3 0.2 - - - -
698B GLY* 1.3 74.7 - - - +
700B LEU* 1.3 62.2 + - - +
702B ASN* 3.2 18.9 + - - +
720B ARG* 3.5 19.0 - - - +
721B GLU 3.5 22.4 - - - -
722B LEU* 3.4 18.9 - - - +
723B TYR 4.7 0.9 - - - -
724B GLY 5.8 0.4 - - - -
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Residues in contact with LEU 700 (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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278B LEU* 3.9 13.8 - - + +
587B ILE* 4.5 2.7 - - + -
682B PHE* 3.8 31.0 - - + +
685B PRO* 4.6 9.2 - - + -
686B MET* 3.4 37.2 - - + -
695B ALA* 4.2 23.1 - - + +
696B ASP 3.2 21.4 + - - +
697B ALA* 3.1 12.2 + - - +
699B GLY* 1.3 72.3 - - - +
701B VAL* 1.3 62.3 + - - +
702B ASN 3.0 2.9 - - - -
703B HIS* 3.1 22.2 + - + +
706B LEU* 3.9 1.4 - - - +
722B LEU* 4.3 14.4 - - + -
723B TYR* 4.9 4.5 - - + +
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Residues in contact with VAL 701 (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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275B LYS* 3.4 42.0 + - + +
278B LEU* 3.7 23.8 - - + -
279B LEU* 3.9 24.9 - - + +
697B ALA 3.0 20.6 + - - +
698B GLY* 3.1 12.2 + - - +
700B LEU* 1.3 78.7 - - - +
702B ASN* 1.3 59.1 + - - +
703B HIS 3.3 1.4 + - - +
706B LEU* 4.2 8.4 - - - +
715B ILE* 4.3 1.2 - - + +
716B ARG* 4.1 12.6 - - - -
717B VAL* 3.7 23.3 - - + -
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Residues in contact with ASN 702 (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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698B GLY 3.8 5.4 + - - -
699B GLY 3.4 13.8 + - - +
700B LEU 3.0 1.0 - - - -
701B VAL* 1.3 76.8 - - - +
703B HIS* 1.3 64.5 + - - +
704B PRO* 3.5 5.9 - - - +
707B LYS* 6.1 0.2 - - - +
715B ILE 5.5 0.7 - - - -
716B ARG* 2.9 18.6 - - + +
717B VAL 2.8 46.0 + - - -
720B ARG 3.1 17.6 + - - -
722B LEU* 3.9 16.9 - - + +
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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