Contacts of the helix formed by residues 3173 - 3182 (chain D) in PDB entry 1PXX
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 ASP3173 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3171D LEU 3.7 1.2 + - - -
3172D PRO* 1.3 70.4 - - - +
3174D SER* 1.3 64.4 + - - +
3175D LYS* 2.6 42.3 + - - +
3176D GLU* 3.4 31.9 - - + +
3177D VAL* 3.0 24.4 + - - +
3449D LYS* 5.3 0.9 + - - -
3456D ARG* 4.6 1.1 - - - +
3494D LEU* 5.2 1.0 - - + +
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Residues in contact with SER3174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3172D PRO 3.1 5.6 + - - -
3173D ASP* 1.3 74.8 + - - +
3175D LYS* 1.3 52.3 + - - +
3177D VAL* 3.5 8.8 - - - +
3178D LEU* 2.7 36.1 + - - +
3449D LYS* 2.7 34.6 + - - -
3452D ILE* 3.6 27.3 - - - +
3453D ASP* 3.0 18.0 + - - -
3456D ARG* 3.7 10.0 - - - +
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Residues in contact with LYS3175 (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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3173D ASP* 2.6 24.8 + - - +
3174D SER* 1.3 77.3 + - - +
3176D GLU* 1.3 62.6 + - - +
3178D LEU* 3.4 10.9 - - + +
3179D GLU* 2.9 61.6 + - + +
3449D LYS* 4.2 19.7 - - - +
3703D BOG 4.5 9.9 + - - -
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Residues in contact with GLU3176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3173D ASP* 3.2 35.1 + - + +
3175D LYS* 1.3 85.3 - - - +
3177D VAL* 1.3 61.5 + - - +
3179D GLU* 4.2 12.3 - - - +
3180D LYS* 2.9 70.4 + - - +
3494D LEU* 3.8 15.0 - - + -
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Residues in contact with VAL3177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3172D PRO* 4.1 16.6 - - + -
3173D ASP 3.0 19.2 + - - +
3174D SER* 3.2 9.6 + - - +
3176D GLU* 1.3 72.7 - - - +
3178D LEU* 1.3 68.6 + - - +
3181D VAL* 3.2 32.8 + - + +
3182D LEU* 3.7 3.9 + - + +
3452D ILE* 4.0 17.3 - - + -
3456D ARG* 4.2 2.9 - - - +
3491D LEU* 5.0 1.8 - - + -
3494D LEU* 4.3 13.5 - - + -
3495D TYR* 3.7 30.7 - - + +
3505D PRO* 4.1 15.5 - - + -
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Residues in contact with LEU3178 (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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3174D SER 2.7 21.6 + - - +
3175D LYS* 3.4 11.9 - - + +
3177D VAL* 1.3 73.0 - - - +
3179D GLU* 1.3 61.3 + - + +
3182D LEU* 3.0 30.2 + - + +
3183D LEU* 2.9 48.0 + - + -
3440D VAL* 5.3 0.2 - - + -
3445D GLN* 3.6 41.3 - - + +
3448D ALA* 4.2 17.0 - - + -
3449D LYS* 4.2 22.4 - - + +
3452D ILE* 4.4 2.0 - - + +
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Residues in contact with GLU3179 (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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3175D LYS* 2.9 53.0 + - - +
3176D GLU* 4.2 11.0 - - - +
3178D LEU* 1.3 81.0 - - + +
3180D LYS* 1.3 59.4 + - + +
3183D LEU* 3.7 19.3 - - + +
3185D ARG* 2.8 30.7 + - - -
3445D GLN* 5.1 2.2 - - - +
3703D BOG 2.8 60.7 + - - +
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Residues in contact with LYS3180 (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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3176D GLU* 2.9 58.2 + - + +
3177D VAL 4.5 0.7 - - - +
3179D GLU* 1.3 75.8 - - + +
3181D VAL* 1.3 63.0 + - + +
3185D ARG* 3.1 2.8 + - - +
3438D ARG* 2.7 33.1 + - - -
3490D GLU* 3.2 35.7 - - + +
3494D LEU* 4.1 24.7 - - + +
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Residues in contact with VAL3181 (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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3177D VAL* 3.2 22.8 + - + +
3180D LYS* 1.3 84.1 - - + +
3182D LEU* 1.3 66.9 + - + +
3185D ARG* 4.7 0.2 - - - -
3438D ARG* 2.8 32.2 + - - +
3487D MET* 3.4 40.8 - - + +
3490D GLU* 4.0 10.1 - - + -
3491D LEU* 3.7 26.0 - - + -
3494D LEU* 5.6 0.9 - - + -
3505D PRO* 5.8 1.8 - - + -
3509D VAL* 3.7 22.5 - - + +
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Residues in contact with LEU3182 (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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3177D VAL* 3.9 11.4 - - + +
3178D LEU* 3.0 29.5 + - + +
3181D VAL* 1.3 91.4 - - + +
3183D LEU* 1.3 66.5 + - - +
3438D ARG* 3.7 1.6 - - - +
3439D ASN 3.1 7.6 + - - -
3440D VAL* 2.9 30.5 + - + +
3448D ALA* 5.1 4.5 - - + -
3452D ILE* 4.0 29.2 - - + -
3504D TYR* 4.6 11.2 - - + -
3505D PRO* 4.4 17.3 - - + +
3508D LEU* 3.8 34.3 - - + +
3509D VAL* 4.8 4.3 - - + -
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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