Contacts of the helix formed by residues 3665 - 3674 (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 PHE3665 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2126D HIS* 4.9 2.2 - + - -
2129D TYR* 3.5 40.0 + + + +
2130D ASP* 3.5 34.1 - - + -
2132D LEU* 5.9 7.6 - - + -
2133D GLY 6.0 1.8 - - - -
3663D HIS* 3.4 29.3 - - + -
3664D SER* 1.3 75.2 - - - +
3666D GLU* 1.3 64.0 + - - +
3667D ASP* 3.2 4.6 + - - -
3668D ARG* 3.8 4.7 + - + +
3669D MET* 3.4 19.8 + - + +
3724D ILE* 3.6 33.7 - - + -
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Residues in contact with GLU3666 (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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3664D SER* 3.1 7.7 - - - +
3665D PHE* 1.3 79.3 - - - +
3667D ASP* 1.3 64.0 + - - +
3669D MET 4.2 0.7 - - - -
3670D ILE* 3.4 13.9 + - - +
3724D ILE* 3.2 39.4 - - + +
3727D LYS* 3.9 21.1 - - + -
3728D SER* 3.2 21.3 - - - +
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Residues in contact with ASP3667 (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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3664D SER 4.3 5.0 + - - +
3665D PHE 3.2 1.4 - - - -
3666D GLU* 1.3 78.4 - - - +
3668D ARG* 1.3 63.8 + - - +
3669D MET 3.1 1.6 + - - -
3670D ILE* 3.3 12.3 + - - +
3671D ASP* 2.7 31.9 + - - +
3728D SER* 4.5 9.3 - - - +
3731D LEU 6.0 4.1 - - - -
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Residues in contact with ARG3668 (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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2129D TYR* 3.4 20.5 + - - +
3665D PHE* 3.8 4.8 + - - +
3667D ASP* 1.3 82.2 - - - +
3669D MET* 1.3 61.3 + - - +
3670D ILE 3.3 0.4 - - - -
3671D ASP* 3.8 9.3 - - - +
3672D ASP* 3.6 23.7 + - - +
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Residues in contact with MET3669 (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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2125D LEU* 6.0 4.1 - - + +
2129D TYR* 3.6 25.9 + - + -
3665D PHE* 3.4 19.6 + - + +
3666D GLU 4.4 4.7 - - - +
3667D ASP 3.1 1.6 + - - -
3668D ARG* 1.3 77.6 - - - +
3670D ILE* 1.3 65.5 + - + +
3672D ASP* 4.5 1.4 - - - +
3673D LEU* 3.4 23.2 + - - +
3724D ILE* 4.4 15.0 - - + -
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Residues in contact with ILE3670 (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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3666D GLU 3.4 18.6 - - - +
3667D ASP 3.3 6.3 + - - +
3669D MET* 1.3 82.3 - - + +
3671D ASP* 1.3 65.4 + - - +
3673D LEU* 3.5 6.4 + - + +
3674D SER* 3.1 21.8 + - - -
3694D LEU* 3.9 21.9 - - + +
3721D TYR* 6.3 2.9 - - + -
3724D ILE* 4.7 9.4 - - + +
3725D MET* 4.4 25.1 - - + -
3728D SER* 3.6 21.5 - - - +
3764D ARG* 3.6 29.6 + - - -
3765D LEU* 5.5 4.9 - - + -
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Residues in contact with ASP3671 (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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3667D ASP* 2.7 38.7 + - - +
3668D ARG* 3.8 6.7 + - - +
3669D MET 3.6 0.2 - - - -
3670D ILE* 1.3 77.6 - - - +
3672D ASP* 1.3 58.1 + - - +
3674D SER* 3.1 3.3 + - - -
3675D LYS* 2.9 30.2 + - - +
3764D ARG* 3.5 34.1 + - - +
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Residues in contact with ASP3672 (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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2104D VAL* 4.6 13.0 - - + +
3668D ARG 3.6 16.4 + - - +
3669D MET* 5.0 1.1 - - - +
3670D ILE 3.4 0.2 - - - -
3671D ASP* 1.3 79.5 - - - +
3673D LEU* 1.3 61.9 + - - +
3675D LYS* 3.6 17.6 + - - +
3676D ALA 4.9 1.0 + - - -
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Residues in contact with LEU3673 (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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2104D VAL* 4.1 24.2 - - + +
2107D ALA* 5.6 3.8 - - + -
2122D PHE* 5.3 9.9 - - + -
2125D LEU* 4.4 25.4 - - + -
3669D MET 3.4 20.1 + - - +
3670D ILE* 3.5 7.1 + - + +
3671D ASP 3.2 0.8 - - - -
3672D ASP* 1.3 79.0 - - - +
3674D SER* 1.3 58.5 + - - +
3675D LYS 3.5 0.6 + - - -
3676D ALA 5.2 0.4 + - - -
3693D PRO* 3.2 40.3 - - + +
3694D LEU* 3.8 24.3 + - + -
3697D LEU* 3.9 26.5 - - + -
3721D TYR* 5.4 2.9 - - + -
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Residues in contact with SER3674 (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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3670D ILE 3.1 17.4 + - - -
3671D ASP 3.4 3.4 - - - -
3673D LEU* 1.3 76.3 - - - +
3675D LYS* 1.3 64.7 + - - +
3676D ALA* 3.6 4.2 - - - -
3692D ASP* 5.2 5.5 - - - +
3693D PRO* 5.2 3.1 - - - -
3694D LEU* 3.6 36.0 + - - +
3764D ARG* 4.9 13.1 + - - +
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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