Contacts of the helix formed by residues 3969 - 3978 (chain F) in PDB entry 6X34
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 THR3969 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3967F PRO 5.8 0.4 - - - -
3968F CYS* 1.3 79.3 - - - +
3970F GLY* 1.3 75.8 + - - +
3971F ASN 3.2 2.1 + - - -
3972F GLN* 3.5 2.2 + - - +
3973F GLN* 2.7 38.0 - - - +
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Residues in contact with GLY3970 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3896F ASN* 6.4 1.3 - - - -
3899F ARG* 4.4 21.0 - - - +
3969F THR* 1.3 84.3 + - - +
3971F ASN* 1.3 62.9 + - - +
3973F GLN* 4.4 2.1 - - - +
3974F SER* 3.3 27.7 + - - -
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Residues in contact with ASN3971 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3895F GLN* 4.0 27.7 + - - +
3896F ASN* 5.3 1.2 - - - -
3898F LEU* 5.9 0.4 - - - +
3899F ARG* 5.3 3.2 - - - +
3911F ILE* 4.5 20.9 - - - +
3963F TYR* 3.1 50.5 + - + +
3964F ILE* 4.6 5.2 - - + +
3968F CYS* 3.6 21.8 - - - +
3969F THR 3.2 0.8 - - - +
3970F GLY* 1.3 81.3 + - - +
3972F GLN* 1.3 59.6 + - - +
3974F SER* 4.0 2.8 - - - -
3975F LEU* 3.2 30.7 + - - +
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Residues in contact with GLN3972 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3964F ILE* 5.2 6.5 - - + +
3967F PRO* 5.2 2.3 - - - +
3968F CYS* 3.2 42.6 + - - +
3969F THR* 3.5 1.7 + - - +
3970F GLY 3.4 0.2 - - - -
3971F ASN* 1.3 76.1 - - - +
3973F GLN* 1.3 76.1 + - - +
3975F LEU* 4.0 3.0 - - - +
3976F ALA* 3.1 25.8 + - - +
4024F SER 5.3 2.3 - - - +
4025F LEU* 4.0 30.5 + - + +
4028F GLY 4.9 7.4 + - - +
4029F ASN* 5.4 9.5 - - - +
4035F ILE* 4.8 26.0 - - + +
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Residues in contact with GLN3973 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3969F THR* 2.7 28.9 + - - +
3970F GLY* 4.8 2.0 - - - +
3972F GLN* 1.3 86.5 + - - +
3974F SER* 1.3 65.0 + - - +
3976F ALA* 4.6 3.4 - - - -
3977F HIS* 3.1 47.6 + - + +
4034F MET* 6.3 2.0 - - - -
4035F ILE* 4.9 20.5 - - + +
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Residues in contact with SER3974 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3899F ARG* 5.3 3.2 - - - +
3909F ASN* 4.4 16.8 + - - -
3911F ILE* 4.2 25.1 - - - +
3912F ILE* 6.1 2.5 - - - -
3970F GLY 3.3 20.6 + - - -
3971F ASN 4.3 1.6 - - - -
3972F GLN 3.3 0.6 - - - -
3973F GLN* 1.3 77.9 - - - +
3975F LEU* 1.3 63.3 + - - +
3977F HIS* 3.6 4.3 + - - +
3978F SER* 3.1 25.1 + - - -
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Residues in contact with LEU3975 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3911F ILE* 5.1 7.3 - - + +
3915F VAL* 5.2 2.7 - - + -
3960F LEU* 4.1 37.2 - - + +
3964F ILE* 5.5 8.3 - - + -
3971F ASN 3.2 19.1 + - - +
3972F GLN* 4.1 3.8 - - - +
3973F GLN 3.4 0.2 - - - -
3974F SER* 1.3 76.7 - - - +
3976F ALA* 1.3 61.9 + - - +
3978F SER* 2.8 20.5 + - - +
3980F LEU* 3.7 26.4 - - + +
3981F TRP 5.0 1.4 + - - +
4025F LEU* 3.7 29.6 - - + -
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Residues in contact with ALA3976 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3972F GLN 3.1 18.6 + - - +
3973F GLN* 3.6 5.4 + - - +
3975F LEU* 1.3 81.3 - - - +
3977F HIS* 1.3 68.9 + - + +
3978F SER 3.5 6.8 + - - +
3981F TRP* 5.9 2.6 - - - +
4025F LEU* 6.2 3.4 - - + -
4035F ILE* 5.3 13.2 - - + -
4038F GLN* 4.6 26.8 - - + +
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Residues in contact with HIS3977 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3973F GLN* 3.1 34.2 + - + +
3974F SER* 4.2 4.5 - - - +
3975F LEU 3.4 0.2 - - - -
3976F ALA* 1.3 81.3 - - + +
3978F SER* 1.3 65.5 + - - +
4034F MET* 5.7 10.1 - - + -
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Residues in contact with SER3978 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3911F ILE* 6.2 0.4 - - - -
3912F ILE* 6.0 2.9 - - - -
3915F VAL* 3.7 28.5 - - - +
3974F SER 3.1 15.6 + - - -
3975F LEU* 2.8 26.7 + - - +
3976F ALA 3.3 8.4 - - - +
3977F HIS* 1.3 82.4 - - - +
3979F ARG* 1.3 60.2 + - - +
3980F LEU* 3.3 12.0 + - - +
3981F TRP* 4.7 3.6 + - - +
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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