Contacts of the helix formed by residues 4038 - 4046 (chain D) 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 GLN4038 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3976D ALA* 4.6 24.1 - - + +
3981D TRP* 5.6 3.3 - - - +
4034D MET* 2.9 28.5 + - - +
4035D ILE* 3.3 14.8 - - + +
4036D ALA 3.1 1.2 - - - -
4037D ARG* 1.3 83.5 + - - +
4039D MET* 1.3 71.9 + - - +
4040D VAL 3.3 0.4 - - - -
4041D ASP* 3.2 19.2 + - - +
4042D MET* 3.3 12.6 + - - +
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Residues in contact with MET4039 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4022D LEU* 4.0 31.2 - - + +
4025D LEU* 3.7 30.7 - - + -
4026D LEU* 3.7 20.9 - - + -
4035D ILE 3.3 22.9 - - - +
4036D ALA* 3.5 20.9 - - - +
4037D ARG 3.6 0.2 - - - -
4038D GLN* 1.3 82.0 - - - +
4040D VAL* 1.3 62.1 + - - +
4042D MET* 3.2 14.9 + - - +
4043D LEU* 3.3 21.8 - - + +
4145D LEU* 4.2 20.4 - - + -
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Residues in contact with VAL4040 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4036D ALA 4.3 6.5 - - - +
4037D ARG* 3.3 31.4 - - + +
4039D MET* 1.3 77.0 - - - +
4041D ASP* 1.3 62.9 + - - +
4042D MET 3.3 0.4 + - - -
4043D LEU* 3.7 11.6 + - - +
4044D VAL* 3.7 17.8 + - - +
4145D LEU* 4.2 23.3 - - + +
4149D VAL* 3.8 30.1 - - + -
4152D ASP* 5.4 9.9 - - + -
4154D ARG* 5.1 5.7 - - + +
4155D LEU* 5.5 4.7 - - + -
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Residues in contact with ASP4041 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4037D ARG 3.7 12.3 - - - +
4038D GLN* 3.2 16.8 + - - +
4039D MET 3.2 0.8 - - - -
4040D VAL* 1.3 81.8 - - + +
4042D MET* 1.3 59.8 + - - +
4043D LEU 3.4 0.2 - - - -
4044D VAL* 3.8 15.7 + - - +
4045D GLU* 4.3 9.4 + - - +
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Residues in contact with MET4042 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3981D TRP* 5.0 20.6 - - + +
3984D VAL* 5.8 4.5 - - + -
3985D VAL* 5.4 5.6 - - + +
4022D LEU* 6.5 1.6 - - + -
4038D GLN 3.3 9.3 + - - +
4039D MET* 3.2 13.2 + - - +
4041D ASP* 1.3 77.8 - - - +
4043D LEU* 1.3 56.2 + - + +
4044D VAL 3.3 1.1 - - - -
4045D GLU* 3.9 4.9 + - - +
4046D SER* 2.5 34.5 + - - -
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Residues in contact with LEU4043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4039D MET* 3.3 17.7 + - + +
4040D VAL* 3.7 10.1 + - - +
4041D ASP 3.4 1.0 - - - -
4042D MET* 1.3 80.4 - - + +
4044D VAL* 1.3 52.1 + - + +
4045D GLU 3.5 0.2 - - - -
4046D SER* 3.3 9.6 - - - +
4047D SER* 2.6 34.7 + - - -
4050D VAL* 5.0 12.7 - - + +
4145D LEU* 4.3 25.1 - - + -
4154D ARG* 4.9 13.9 - - + +
4155D LEU* 5.4 5.2 - - - -
4158D PHE* 3.9 28.3 - - + -
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Residues in contact with VAL4044 (chain D).
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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4040D VAL 3.7 16.6 - - - +
4041D ASP* 3.8 10.3 + - - +
4042D MET 3.3 0.8 - - - -
4043D LEU* 1.3 77.7 - - - +
4045D GLU* 1.3 64.0 + - + +
4047D SER* 2.7 20.7 + - - +
4154D ARG* 4.4 17.9 - - + -
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Residues in contact with GLU4045 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 5.7 4.9 - - - +
3985D VAL* 4.8 19.5 - - + +
4041D ASP 4.3 8.8 + - - +
4042D MET* 3.9 6.1 + - - +
4043D LEU 3.5 0.2 - - - -
4044D VAL* 1.3 83.4 - - + +
4046D SER* 1.3 57.1 + - - +
4047D SER 3.3 1.9 + - - -
4048D SER* 4.6 2.4 + - - -
4049D ASN* 3.4 12.0 + - - -
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Residues in contact with SER4046 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3985D VAL* 4.3 16.6 - - - -
3988D LEU* 5.5 6.1 - - - -
4042D MET 2.5 24.7 + - - -
4043D LEU* 3.3 12.8 - - - +
4044D VAL 3.3 0.4 - - - -
4045D GLU* 1.3 76.5 - - - +
4047D SER* 1.3 54.8 + - - +
4048D SER 3.3 2.7 - - - -
4049D ASN* 3.0 18.2 + - - +
4050D VAL* 2.7 50.2 + - - +
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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