Contacts of the helix formed by residues 709 - 719 (chain A) in PDB entry 1PD0
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 MET 709 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A PRO* 4.7 2.5 - - - -
150A PRO* 3.8 23.8 - - - +
151A ILE* 3.3 22.4 - - - -
153A ASP* 3.4 26.0 - - + +
154A LEU* 3.1 51.6 - - + +
648A GLN* 2.8 20.0 + - - +
708A ARG* 1.3 81.5 - - - +
710A PHE* 1.3 65.0 + - - +
711A PRO 3.5 0.4 - - - -
712A LEU* 3.2 28.9 + - + +
713A LEU* 2.9 27.6 + - + +
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Residues in contact with PHE 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A GLN* 3.6 19.5 + - + -
651A ILE* 3.4 26.9 - - + -
652A ALA* 3.9 12.3 - - + -
655A TYR* 3.7 13.9 - + - -
678A SER* 3.7 20.2 - - - -
679A VAL* 3.9 15.3 - - + -
682A ILE* 3.3 34.1 - - + -
703A LEU* 5.4 1.1 - - + -
707A LEU* 3.0 24.7 + - + +
709A MET* 1.3 77.0 - - - +
711A PRO* 1.3 72.6 - - + +
713A LEU* 3.0 16.4 + - - +
714A MET* 3.0 40.7 + - + +
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Residues in contact with PRO 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.9 23.1 - - + -
679A VAL* 4.1 24.0 - - + -
683A LEU* 4.7 4.5 - - + -
703A LEU* 4.0 8.1 - - + -
707A LEU 3.3 9.4 - - - +
708A ARG 3.9 6.7 - - - +
709A MET 3.7 2.5 - - - -
710A PHE* 1.3 97.3 - - + +
712A LEU* 1.3 55.4 + - - +
714A MET* 3.4 0.9 + - - +
715A HIS* 2.9 32.2 + - - +
913A TYR* 3.9 15.0 - - - +
916A PHE* 3.6 10.2 - - + -
917A LEU* 4.1 12.6 - - + -
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Residues in contact with LEU 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 3.6 26.9 - - + -
151A ILE* 4.3 1.3 - - + -
154A LEU* 5.8 0.9 - - + -
708A ARG 5.1 0.7 - - - +
709A MET* 3.2 33.1 + - + +
710A PHE 3.2 0.2 - - - -
711A PRO* 1.3 80.6 - - - +
713A LEU* 1.3 59.1 + - + +
715A HIS* 4.0 0.2 - - - +
716A SER* 2.7 44.1 + - - +
753A TYR* 3.8 24.0 - - + -
904A GLU* 4.0 16.8 - - + -
913A TYR* 3.5 47.2 + - + +
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Residues in contact with LEU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU* 3.9 22.2 - - + -
648A GLN 4.8 2.9 - - - +
649A LEU* 3.6 31.0 - - + -
652A ALA* 3.9 17.9 - - + -
709A MET* 2.9 25.1 + - + +
710A PHE* 3.0 6.7 + - - +
712A LEU* 1.3 78.1 - - + +
714A MET* 1.3 72.0 + - + +
716A SER 3.5 0.2 + - - -
717A LEU* 2.8 28.2 + - - +
749A ILE* 4.1 17.3 - - + +
752A ILE* 3.4 19.0 - - + +
753A TYR* 4.1 19.7 - - + -
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Residues in contact with MET 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ALA* 3.7 36.1 - - + +
655A TYR* 3.9 20.2 - - - -
675A ILE* 3.3 27.8 - - + +
676A ASN* 5.8 0.7 - - - -
678A SER* 3.6 12.1 - - - +
679A VAL* 3.3 27.1 - - + -
710A PHE* 3.0 35.8 + - + +
713A LEU* 1.3 81.9 - - + +
715A HIS* 1.3 70.1 + - - +
717A LEU* 3.0 26.9 + - + +
718A THR* 3.0 9.4 + - - +
752A ILE* 5.3 3.6 - - + -
916A PHE* 5.5 0.2 - - - -
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Residues in contact with HIS 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A ASN* 5.3 1.0 + - - -
711A PRO 2.9 17.9 + - - +
712A LEU 4.0 2.9 - - - +
714A MET* 1.3 74.8 - - - +
716A SER* 1.3 66.8 + - - +
718A THR* 2.5 36.6 + - - -
719A LYS* 2.9 44.9 + - - +
903A VAL 4.1 3.6 - - - -
910A ASN* 5.8 0.9 - - + -
911A GLU* 3.3 25.7 + - - -
912A SER 3.5 6.7 + - - -
913A TYR* 3.6 27.4 - + + -
916A PHE* 3.4 46.6 - + + -
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Residues in contact with SER 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A LEU* 2.7 28.8 + - - +
713A LEU* 3.8 4.5 - - - -
715A HIS* 1.3 78.6 - - - +
717A LEU* 1.3 62.7 + - - +
719A LYS* 3.0 15.7 + - - +
720A HIS* 3.3 8.5 + - - +
752A ILE* 3.9 17.9 - - - +
753A TYR* 3.8 9.1 - - - -
903A VAL* 3.2 45.8 + - - +
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Residues in contact with LEU 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A TYR 4.8 0.4 - - - +
656A ASN* 4.0 28.0 - - + +
675A ILE* 3.8 27.4 - - + -
713A LEU 2.8 16.4 + - - +
714A MET* 3.0 31.2 + - + +
716A SER* 1.3 77.4 - - - +
718A THR* 1.3 53.7 + - - +
720A HIS* 2.7 34.1 + - + +
723A PHE* 3.7 27.6 - - + -
740A LEU* 3.9 15.5 - - + -
752A ILE* 3.8 21.5 - - + +
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Residues in contact with THR 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A ARG* 4.6 15.9 - - - +
675A ILE* 3.5 28.5 - - + -
676A ASN* 3.8 29.2 - - - +
714A MET 3.0 14.9 + - - +
715A HIS* 2.5 27.5 + - - +
717A LEU* 1.3 74.7 - - - +
719A LYS* 1.3 62.8 + - - +
720A HIS 3.4 0.2 - - - -
723A PHE* 3.9 6.4 - - - +
724A ARG* 3.5 22.6 + - - -
725A SER 4.7 0.7 + - - -
910A ASN* 5.4 2.6 + - - -
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Residues in contact with LYS 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A HIS* 2.9 44.7 + - - +
716A SER* 3.0 7.6 + - - +
717A LEU 3.0 1.2 - - - -
718A THR* 1.3 81.4 - - - +
720A HIS* 1.3 65.9 + - - +
724A ARG* 3.1 24.0 + - - +
900A SER 5.2 4.8 - - - +
903A VAL* 2.9 41.1 + - + +
904A GLU 4.0 2.6 - - - -
905A ASP 2.6 30.9 + - - +
907A ILE* 4.7 15.2 - - + +
910A ASN* 4.5 24.0 - - + +
911A GLU 3.1 10.9 + - - -
912A SER* 4.1 0.2 - - - +
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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