Contacts of the helix formed by residues 3694 - 3706 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3670B ILE* 3.9 29.2 - - + +
3673B LEU* 3.8 28.5 + - + -
3674B SER* 3.6 34.3 + - - +
3692B ASP* 3.2 3.8 - - + +
3693B PRO* 1.3 78.0 - - - +
3695B HIS* 1.3 62.4 + - - +
3696B GLN 3.3 0.4 - - - -
3697B LEU* 3.4 30.2 + - + +
3698B VAL* 4.2 6.8 + - - +
3725B MET* 5.8 5.6 - - + -
3764B ARG* 4.4 18.2 - - + +
3765B LEU* 4.7 14.4 - - + -
3768B ARG* 5.0 4.5 - - - +
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Residues in contact with HIS3695 (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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3691B PRO* 4.3 18.2 - - + -
3692B ASP* 2.9 28.8 + - + +
3694B LEU* 1.3 80.4 - - - +
3696B GLN* 1.3 61.4 + - - +
3697B LEU 3.4 0.2 - - - -
3698B VAL* 3.7 3.6 + - + +
3699B LEU* 3.3 55.8 + - + +
3767B ASN 5.4 0.9 - - - -
3768B ARG* 3.6 24.4 - - + +
3769B GLY* 3.8 19.7 + - - -
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Residues in contact with GLN3696 (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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2107B ALA* 4.2 17.8 + - - +
2110B ASP 5.0 0.8 + - - -
2111B PHE* 3.8 33.3 - - + +
2112B VAL* 5.1 15.0 - - + -
2118B VAL* 4.8 6.7 - - + +
2122B PHE* 4.3 14.4 - - + -
3691B PRO* 3.6 26.8 + - + +
3692B ASP 3.0 26.2 + - - +
3693B PRO* 3.1 19.4 - - - +
3694B LEU 3.3 1.0 - - - -
3695B HIS* 1.3 78.3 - - - +
3697B LEU* 1.3 60.3 + - - +
3699B LEU* 3.2 6.1 + - + +
3700B HIS* 2.8 30.5 + - - +
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Residues in contact with LEU3697 (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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2122B PHE* 3.5 33.9 - - + -
3673B LEU* 3.9 20.9 - - + -
3693B PRO 3.4 17.3 - - - +
3694B LEU* 3.4 36.6 - - + +
3696B GLN* 1.3 76.3 - - - +
3698B VAL* 1.3 62.1 + - - +
3700B HIS* 3.3 7.6 + - - +
3701B PHE* 3.1 35.1 + - + -
3721B TYR* 4.3 27.6 - - + -
3725B MET* 5.1 17.7 - - + -
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Residues in contact with VAL3698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3694B LEU 4.2 4.8 + - - +
3695B HIS 3.7 10.3 + - - +
3696B GLN 3.3 0.2 - - - -
3697B LEU* 1.3 79.0 - - - +
3699B LEU* 1.3 64.4 + - + +
3701B PHE* 4.2 2.2 + - - +
3702B SER* 3.8 15.2 + - - -
3768B ARG* 4.9 3.8 - - + -
3769B GLY* 3.5 41.6 - - - +
3770B ALA* 4.0 9.4 - - + +
3773B MET* 4.3 12.5 - - + +
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Residues in contact with LEU3699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2111B PHE* 4.8 22.2 - - + -
3695B HIS* 3.3 50.0 + - + +
3696B GLN* 3.2 6.6 + - - +
3697B LEU 3.2 0.4 - - - -
3698B VAL* 1.3 79.0 - - + +
3700B HIS* 1.3 60.8 + - - +
3702B SER* 2.5 27.3 + - - +
3703B ARG* 3.8 21.5 + - - +
3769B GLY* 5.5 6.1 - - - +
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Residues in contact with HIS3700 (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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2115B PRO* 3.3 36.9 - - + +
2118B VAL* 3.5 18.1 - - + +
2119B ARG* 3.4 42.7 + - + +
2122B PHE* 4.6 16.4 - + + -
3696B GLN 2.8 17.4 + - - +
3697B LEU* 3.3 10.4 + - - +
3699B LEU* 1.3 78.5 - - - +
3701B PHE* 1.3 84.4 + + - +
3702B SER 3.3 0.9 + - - -
3703B ARG* 3.5 19.2 + - - +
3704B THR* 3.8 12.0 + - + +
3717B LEU* 4.5 4.8 - - + +
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Residues in contact with PHE3701 (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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2122B PHE* 6.1 2.2 - + - -
3697B LEU* 3.1 35.8 + - + +
3698B VAL* 4.2 3.8 + - - +
3699B LEU 3.5 0.2 - - - -
3700B HIS* 1.3 91.8 - + + +
3702B SER* 1.3 63.1 + - - +
3703B ARG 3.3 0.2 - - - -
3704B THR* 2.7 30.3 + - + +
3705B ALA* 3.2 12.8 + - - +
3715B ASP* 6.2 0.4 - - + -
3717B LEU* 4.2 24.0 - - + -
3718B TYR* 3.5 68.2 - + + +
3721B TYR* 5.2 14.6 - + + -
3725B MET* 6.3 2.9 - - + -
3773B MET* 5.4 8.3 - - + -
3777B MET* 5.9 0.7 - - - +
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Residues in contact with SER3702 (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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461B HIS* 5.2 1.5 + - - -
462B GLU* 6.1 1.3 - - - -
3698B VAL 3.9 9.4 + - - -
3699B LEU* 2.5 40.3 + - - +
3701B PHE* 1.3 77.7 - - - +
3703B ARG* 1.3 61.8 + - - +
3705B ALA* 3.5 2.2 + - - -
3706B LEU* 3.4 27.5 + - - +
3773B MET* 5.7 5.8 - - - +
3776B GLN* 4.1 17.3 - - - -
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Residues in contact with ARG3703 (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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461B HIS* 3.4 54.8 + - + +
2111B PHE* 5.0 19.4 - - - -
2113B GLN* 5.9 4.1 - - - +
2114B SER 6.3 0.4 - - - -
2115B PRO* 4.9 26.2 - - + +
3699B LEU* 3.8 23.8 + - - +
3700B HIS* 3.5 12.2 + - - +
3701B PHE 3.3 0.4 - - - -
3702B SER* 1.3 77.5 + - - +
3704B THR* 1.3 56.9 + - + +
3706B LEU 3.6 1.1 - - - +
3707B THR* 2.3 38.0 + - - +
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Residues in contact with THR3704 (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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2119B ARG* 3.4 28.9 - - - +
3700B HIS* 3.8 17.3 - - + +
3701B PHE* 2.7 36.3 + - + +
3703B ARG* 1.3 78.7 - - + +
3705B ALA* 1.3 60.1 + - - +
3707B THR* 3.2 14.7 + - - -
3777B MET* 5.8 2.4 - - - -
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Residues in contact with ALA3705 (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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3701B PHE 3.2 12.4 + - - +
3702B SER* 3.9 3.1 - - - +
3703B ARG 3.2 0.2 - - - -
3704B THR* 1.3 83.4 + - - +
3706B LEU* 1.3 75.1 + - + +
3707B THR 3.5 1.5 + - - -
3708B GLU 4.9 4.3 - - - +
3773B MET 6.0 0.2 - - - +
3776B GLN* 4.4 20.0 - - + +
3777B MET* 4.5 16.2 - - + -
3780B ALA* 3.9 22.5 - - + +
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Residues in contact with LEU3706 (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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461B HIS* 4.5 5.9 + - + +
462B GLU* 5.3 16.6 - - + -
465B GLN* 3.5 28.1 + - + +
3702B SER 3.4 13.7 + - - +
3703B ARG* 3.6 4.4 - - - +
3705B ALA* 1.3 88.3 - - + +
3707B THR* 1.3 61.9 + - - +
3708B GLU 3.8 2.2 - - - -
3776B GLN* 3.4 42.4 - - + +
3814B TYR* 5.4 3.1 - - - +
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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