Contacts of the helix formed by residues 3694 - 3706 (chain H) 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 LEU3694 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3670H ILE* 3.9 30.1 - - + +
3673H LEU* 3.8 28.3 + - + -
3674H SER* 3.6 33.8 + - - +
3692H ASP* 3.2 3.7 - - + +
3693H PRO* 1.3 79.0 - - - +
3695H HIS* 1.3 62.3 + - - +
3696H GLN 3.3 0.2 - - - -
3697H LEU* 3.4 29.7 + - + +
3698H VAL* 4.2 6.8 + - - +
3725H MET* 5.8 6.1 - - + -
3764H ARG* 4.4 17.9 - - + +
3765H LEU* 4.7 13.7 - - + -
3768H ARG* 5.0 4.5 - - - +
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Residues in contact with HIS3695 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2111H PHE* 5.8 0.2 - + - -
3691H PRO* 4.3 18.8 - - + -
3692H ASP* 2.9 29.3 + - + +
3694H LEU* 1.3 79.8 - - - +
3696H GLN* 1.3 59.7 + - - +
3697H LEU 3.4 0.2 - - - -
3698H VAL* 3.7 3.6 + - + +
3699H LEU* 3.3 56.5 + - + +
3767H ASN 5.4 0.4 - - - -
3768H ARG* 3.6 25.3 - - + +
3769H GLY* 3.8 18.8 + - - -
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Residues in contact with GLN3696 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2107H ALA* 4.2 17.6 + - - +
2110H ASP 5.0 0.6 + - - -
2111H PHE* 3.8 33.7 - - + +
2112H VAL* 5.1 13.9 - - + -
2118H VAL* 4.8 6.3 - - + -
2122H PHE* 4.3 14.7 - - + -
3691H PRO* 3.6 26.3 + - - +
3692H ASP 3.0 26.9 + - - +
3693H PRO* 3.1 20.0 + - - +
3694H LEU 3.3 0.8 - - - -
3695H HIS* 1.3 77.2 - - - +
3697H LEU* 1.3 59.9 + - - +
3698H VAL 3.3 0.2 - - - -
3699H LEU* 3.5 6.5 - - - +
3700H HIS* 2.8 31.4 + - - +
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Residues in contact with LEU3697 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2122H PHE* 3.5 35.2 - - + -
3673H LEU* 3.9 20.4 - - + -
3693H PRO 3.4 17.3 - - - +
3694H LEU* 3.4 36.6 - - + +
3696H GLN* 1.3 76.0 - - - +
3698H VAL* 1.3 62.3 + - - +
3700H HIS* 3.3 7.7 + - - +
3701H PHE* 3.1 35.5 + - + -
3721H TYR* 4.3 27.6 - - + -
3725H MET* 5.1 16.4 - - + -
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Residues in contact with VAL3698 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3694H LEU 4.2 4.5 + - - +
3695H HIS 3.7 10.1 + - - +
3696H GLN 3.3 0.4 - - - -
3697H LEU* 1.3 78.7 - - - +
3699H LEU* 1.3 62.6 + - + +
3701H PHE* 4.2 2.8 + - - +
3702H SER* 3.8 15.1 + - - -
3768H ARG* 4.9 4.0 - - + -
3769H GLY* 3.5 41.5 - - - +
3770H ALA* 4.0 9.9 - - + +
3773H MET* 4.3 12.9 - - + +
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Residues in contact with LEU3699 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2111H PHE* 4.7 22.0 - - + -
3695H HIS* 3.3 51.3 + - + +
3696H GLN* 3.2 7.4 + - - +
3697H LEU 3.2 0.4 - - - -
3698H VAL* 1.3 79.2 - - + +
3700H HIS* 1.3 60.7 + - - +
3702H SER* 2.5 28.6 + - - +
3703H ARG* 3.8 21.9 + - - +
3769H GLY* 5.5 5.6 - - - +
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Residues in contact with HIS3700 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2115H PRO* 3.3 37.4 - - + +
2118H VAL* 3.5 18.0 - - + +
2119H ARG* 3.4 42.0 + - + +
2122H PHE* 4.6 16.4 - + + -
3696H GLN 2.8 16.9 + - - +
3697H LEU* 3.3 10.7 + - - +
3699H LEU* 1.3 78.1 - - - +
3701H PHE* 1.3 84.8 + + - +
3702H SER 3.3 0.9 + - - -
3703H ARG* 3.5 18.5 + - - +
3704H THR* 3.8 11.7 + - + +
3717H LEU* 4.5 4.8 - - + +
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Residues in contact with PHE3701 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2122H PHE* 6.1 3.1 - + - -
3697H LEU* 3.1 35.4 + - + +
3698H VAL* 4.2 4.5 + - - +
3699H LEU 3.5 0.2 - - - -
3700H HIS* 1.3 90.1 - + - +
3702H SER* 1.3 62.9 + - - +
3703H ARG 3.3 0.2 - - - -
3704H THR* 2.7 30.1 + - + +
3705H ALA* 3.2 13.0 + - - +
3715H ASP* 6.2 0.4 - - + -
3717H LEU* 4.2 23.1 - - + -
3718H TYR* 3.5 68.2 - + + +
3721H TYR* 5.2 13.9 - + + -
3725H MET* 6.3 2.7 - - + -
3773H MET* 5.4 7.4 - - + -
3777H MET* 5.9 1.0 - - - +
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Residues in contact with SER3702 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461H HIS* 5.3 2.2 - - - -
462H GLU* 6.1 1.6 - - - -
3698H VAL 3.9 10.2 + - - -
3699H LEU* 2.5 39.7 + - - +
3701H PHE* 1.3 77.3 - - - +
3703H ARG* 1.3 61.4 + - - +
3705H ALA* 3.5 2.4 + - - -
3706H LEU* 3.4 28.2 + - - +
3773H MET* 5.7 5.6 - - - +
3776H GLN* 4.1 17.9 - - - -
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Residues in contact with ARG3703 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461H HIS* 3.4 55.4 + - + +
2111H PHE* 5.0 19.2 - - - -
2113H GLN* 5.9 3.9 - - - +
2114H SER 6.3 0.2 - - - -
2115H PRO* 4.9 25.8 - - + +
3699H LEU* 3.8 24.0 + - - +
3700H HIS* 3.5 11.7 + - - +
3701H PHE 3.3 0.2 - - - -
3702H SER* 1.3 78.3 + - - +
3704H THR* 1.3 58.0 + - + +
3706H LEU 3.6 0.9 - - - +
3707H THR* 2.3 38.2 + - - +
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Residues in contact with THR3704 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119H ARG* 3.4 29.2 - - - +
3700H HIS* 3.8 17.5 - - + +
3701H PHE* 2.7 36.4 + - + +
3703H ARG* 1.3 77.7 - - + +
3705H ALA* 1.3 59.2 + - - +
3707H THR* 3.2 15.2 + - - -
3777H MET* 5.8 2.4 - - - -
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Residues in contact with ALA3705 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3701H PHE 3.2 12.9 + - - +
3702H SER* 3.9 3.1 - - - +
3703H ARG 3.2 0.6 - - - -
3704H THR* 1.3 83.4 + - - +
3706H LEU* 1.3 74.1 + - + +
3707H THR 3.5 0.7 + - - -
3708H GLU 4.9 4.5 - - - +
3773H MET 6.0 0.2 - - - +
3776H GLN* 4.4 21.1 - - + +
3777H MET* 4.5 15.9 - - + -
3780H ALA* 3.9 22.7 - - + +
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Residues in contact with LEU3706 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461H HIS* 4.5 5.0 + - + +
462H GLU* 5.3 17.0 - - + -
465H GLN* 3.5 28.0 + - + +
3702H SER 3.4 13.1 + - - +
3703H ARG* 3.6 4.7 - - - +
3704H THR 3.4 0.2 - - - -
3705H ALA* 1.3 87.4 - - + +
3707H THR* 1.3 62.2 + - - +
3708H GLU 3.8 2.5 - - - -
3776H GLN* 3.4 42.2 - - + +
3814H TYR* 5.4 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