Contacts of the helix formed by residues 924 - 937 (chain D) in PDB entry 1ZYC
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 THR 924 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922D PHE* 4.3 3.6 - - - +
923D SER* 1.3 90.9 + - - +
925D GLY* 1.3 69.4 + - - +
926D MET* 2.9 39.3 + - + +
927D GLU* 3.2 10.6 + - - +
928D ARG* 3.1 22.0 + - - +
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Residues in contact with GLY 925 (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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924D THR* 1.3 77.3 - - - +
926D MET* 1.3 69.8 + - - +
928D ARG* 3.8 9.6 + - - +
929D VAL* 2.9 31.9 + - - +
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Residues in contact with MET 926 (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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924D THR* 2.9 22.4 - - + +
925D GLY* 1.3 86.0 - - - +
927D GLU* 1.3 67.5 + - - +
928D ARG 3.1 1.3 + - - -
929D VAL* 3.3 10.3 + - + +
930D ASN* 3.0 36.6 + - - +
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Residues in contact with GLU 927 (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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920D TYR* 3.7 20.8 + - - -
921D PRO 4.7 0.7 - - - +
922D PHE* 3.5 6.2 - - - -
923D SER* 2.4 47.6 + - - +
924D THR* 3.2 12.8 + - - +
926D MET* 1.3 78.5 - - - +
928D ARG* 1.3 63.6 + - - +
930D ASN* 3.5 7.4 + - - +
931D ILE* 2.9 45.6 + - + +
945D ASP* 5.5 0.3 - - - +
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Residues in contact with ARG 928 (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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801D HIS* 4.2 19.8 + - - -
886D GLY* 4.6 6.1 + - - -
889D MET* 4.5 10.1 - - - +
890D TYR* 3.2 31.7 + - - -
917D GLU* 3.0 19.5 + - - -
922D PHE* 3.6 38.9 - - + -
924D THR 3.1 14.4 + - - +
925D GLY* 3.9 9.3 + - - +
926D MET 3.1 0.6 - - - -
927D GLU* 1.3 76.5 - - - +
929D VAL* 1.3 70.2 + - - +
931D ILE* 2.8 23.9 + - - +
932D LEU* 2.9 39.0 + - + +
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Residues in contact with VAL 929 (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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889D MET* 4.9 8.4 - - + +
925D GLY 2.9 24.2 + - - +
926D MET* 3.3 13.4 + - + +
928D ARG* 1.3 88.4 - - - +
930D ASN* 1.3 66.1 + - - +
932D LEU* 3.5 6.9 + - - +
933D LYS* 2.8 48.5 + - + +
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Residues in contact with ASN 930 (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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926D MET* 3.0 26.6 + - - +
927D GLU* 3.8 7.0 - - - +
929D VAL* 1.3 83.3 - - - +
931D ILE* 1.3 68.1 + - + +
933D LYS* 3.2 9.1 + - - +
934D LYS* 3.1 27.5 + - - +
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Residues in contact with ILE 931 (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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916D PHE* 3.5 31.9 - - + -
920D TYR* 3.3 33.2 - - + +
922D PHE* 3.8 12.8 - - + -
927D GLU* 2.9 41.5 + - + +
928D ARG* 2.8 9.2 + - - +
930D ASN* 1.3 78.4 - - + +
932D LEU* 1.3 59.5 + - + +
934D LYS* 3.4 4.6 + - - +
935D LEU* 2.9 31.8 + - + +
941D GLU 4.2 2.8 - - - +
943D PRO* 4.0 22.0 - - + -
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Residues in contact with LEU 932 (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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889D MET* 3.8 30.5 - - + -
913D ILE* 4.3 22.9 - - + -
916D PHE* 4.3 13.9 - - + -
917D GLU* 4.8 7.9 - - + -
922D PHE* 5.2 0.7 - - + -
928D ARG* 2.9 59.7 + - + +
929D VAL* 3.9 4.0 - - - +
931D ILE* 1.3 77.3 - - + +
933D LYS* 1.3 65.9 + - - +
935D LEU* 2.7 23.6 + - + +
936D ARG* 2.7 33.3 + - - +
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Residues in contact with LYS 933 (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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889D MET* 3.6 29.9 - - + +
929D VAL* 2.8 44.8 + - + +
930D ASN* 3.2 9.4 + - - +
932D LEU* 1.3 71.8 - - - +
934D LYS* 1.3 60.9 + - + +
936D ARG* 3.2 11.7 + - + +
937D SER* 2.8 29.6 + - - -
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Residues in contact with LYS 934 (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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930D ASN* 3.1 13.8 + - + +
931D ILE* 3.9 3.8 - - - +
933D LYS* 1.3 80.9 - - + +
935D LEU* 1.3 52.5 + - - +
937D SER* 3.4 16.8 + - - -
939D SER* 5.4 2.2 + - - -
941D GLU* 2.6 73.8 + - + +
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Residues in contact with LEU 935 (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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913D ILE* 4.8 10.8 - - + -
916D PHE* 3.6 46.2 - - + -
931D ILE* 2.9 19.1 + - + +
932D LEU* 2.7 23.5 + - + +
934D LYS* 1.3 79.6 - - - +
936D ARG* 1.3 55.1 + - + +
937D SER 3.2 1.6 - - - -
940D ILE* 3.3 27.4 - - + +
941D GLU 3.5 11.0 - - - +
942D PHE* 3.6 25.8 - - + -
943D PRO* 5.3 0.7 - - + -
958D ILE* 5.8 0.7 - - + -
962D ILE* 3.5 33.2 - - + +
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Residues in contact with ARG 936 (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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888D ALA* 2.6 29.4 + - - +
889D MET* 3.5 48.1 + - - +
891D VAL* 2.9 26.9 + - - +
893D THR* 4.9 5.7 - - + +
896D LEU* 6.0 1.6 - - - +
909D TYR* 3.4 25.3 + - - +
913D ILE* 5.1 6.5 - - + +
932D LEU* 2.7 27.5 + - - +
933D LYS* 3.5 13.5 - - + +
935D LEU* 1.3 70.2 - - - +
937D SER* 1.3 66.7 + - - +
938D VAL 3.8 0.2 + - - -
940D ILE* 5.2 0.4 - - - -
962D ILE* 5.9 0.7 - - - -
964D HIS* 3.2 20.5 - - + -
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Residues in contact with SER 937 (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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933D LYS 2.8 15.4 + - - -
934D LYS* 3.4 16.0 + - - +
935D LEU 3.2 1.0 - - - -
936D ARG* 1.3 84.7 - - - +
938D VAL* 1.3 59.1 + - - +
939D SER* 2.5 30.0 + - - -
940D ILE* 2.7 26.0 + - - +
964D HIS* 3.1 6.8 + - - -
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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