Contacts of the helix formed by residues 937 - 958 (chain F) in PDB entry 5ZCS
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 ASN 937 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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933F ILE 5.3 0.2 - - - +
934F GLY* 3.9 28.7 + - - +
935F SER 3.4 4.0 + - - -
936F SER* 1.3 74.9 - - - +
938F TRP* 1.3 57.6 + - - +
939F GLY 3.4 1.8 - - - -
940F LEU* 3.7 20.4 - - + +
941F ASN* 2.9 27.8 + - - +
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Residues in contact with TRP 938 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935F SER 5.3 0.4 + - - -
936F SER* 3.3 5.1 - - - -
937F ASN* 1.3 74.1 - - - +
939F GLY* 1.3 61.2 + - - +
941F ASN* 3.3 7.4 + - - +
942F LEU* 2.9 27.5 + - - +
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Residues in contact with GLY 939 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894F HIS* 5.2 9.0 - - - +
936F SER 4.8 2.0 + - - -
937F ASN 3.4 0.4 - - - -
938F TRP* 1.3 75.8 - - - +
940F LEU* 1.3 60.1 + - - +
942F LEU* 3.7 7.2 - - - +
943F LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 940 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888F HIS 5.7 4.9 - - - +
894F HIS* 6.3 0.7 - - - -
937F ASN* 3.5 23.8 + - + +
938F TRP 3.3 0.6 - - - -
939F GLY* 1.3 75.5 - - - +
941F ASN* 1.3 58.1 + - - +
943F LEU* 3.4 6.5 + - - +
944F GLN* 2.9 28.2 + - - +
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Residues in contact with ASN 941 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937F ASN 2.9 19.1 + - - +
938F TRP* 3.6 7.6 - - - +
939F GLY 3.3 0.4 - - - -
940F LEU* 1.3 74.4 - - - +
942F LEU* 1.3 59.8 + - - +
944F GLN* 3.7 6.1 - - - +
945F GLU* 2.9 28.6 + - - +
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Residues in contact with LEU 942 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938F TRP 2.9 17.4 + - - +
939F GLY* 3.7 8.3 - - - +
940F LEU 3.3 0.2 - - - -
941F ASN* 1.3 77.0 - - - +
943F LEU* 1.3 55.9 + - - +
945F GLU* 3.3 7.1 + - - +
946F GLU* 2.9 29.5 + - - +
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Residues in contact with LEU 943 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894F HIS* 5.0 12.6 - - + +
898F VAL* 4.9 18.2 - - + +
939F GLY 2.9 16.7 + - - +
940F LEU* 3.8 7.6 - - - +
942F LEU* 1.3 75.4 - - - +
944F GLN* 1.3 58.6 + - - +
946F GLU* 3.4 7.1 + - - +
947F ASN* 2.9 29.7 + - - +
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Residues in contact with GLN 944 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927F LEU* 5.3 13.9 - - + -
940F LEU 2.9 17.7 + - - +
941F ASN* 3.7 8.5 - - - +
943F LEU* 1.3 77.7 - - - +
945F GLU* 1.3 57.0 + - - +
947F ASN* 3.4 6.7 + - - +
948F VAL* 2.9 29.6 + - - +
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Residues in contact with GLU 945 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941F ASN 2.9 16.9 + - - +
942F LEU* 3.7 7.4 - - - +
944F GLN* 1.3 77.1 - - - +
946F GLU* 1.3 56.5 + - - +
948F VAL* 3.3 6.2 + - - +
949F ILE* 2.9 29.3 + - - +
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Residues in contact with GLU 946 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898F VAL* 5.1 15.0 - - + +
942F LEU 2.9 17.4 + - - +
943F LEU* 3.8 7.9 - - - +
945F GLU* 1.3 76.8 - - - +
947F ASN* 1.3 55.8 + - - +
949F ILE* 3.7 6.8 + - - +
950F PRO* 3.1 25.1 - - - +
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Residues in contact with ASN 947 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901F ILE* 6.1 4.7 - - + -
920F ILE* 5.9 8.9 - - + +
923F LEU* 6.0 6.7 - - + -
943F LEU 2.9 17.4 + - - +
944F GLN* 3.8 7.6 - - - +
945F GLU 3.2 0.2 - - - -
946F GLU* 1.3 76.8 - - - +
948F VAL* 1.3 54.9 + - - +
950F PRO* 3.3 7.5 - - - +
951F ASP* 2.7 34.4 + - - +
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Residues in contact with VAL 948 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944F GLN 2.9 17.7 + - - +
945F GLU* 3.3 6.9 + - - +
947F ASN* 1.3 74.3 - - - +
949F ILE* 1.3 60.9 + - - +
951F ASP* 3.8 8.3 - - - +
952F ILE* 3.0 27.4 + - - +
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Residues in contact with ILE 949 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945F GLU 2.9 16.8 + - - +
946F GLU* 3.9 7.0 - - - +
948F VAL* 1.3 77.0 - - - +
950F PRO* 1.3 57.7 - - - +
952F ILE* 3.3 7.2 + - - +
953F LEU* 2.9 27.5 + - - +
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Residues in contact with PRO 950 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901F ILE* 6.1 2.9 - - + -
902F ILE* 5.2 17.3 - - + +
905F LEU* 6.0 3.5 - - + +
946F GLU 3.1 19.1 - - - +
947F ASN* 3.3 8.0 - - - +
949F ILE* 1.3 75.2 - - - +
951F ASP* 1.3 59.4 + - - +
953F LEU* 3.3 7.9 + - + +
954F LYS* 2.9 28.9 + - - +
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Residues in contact with ASP 951 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920F ILE* 6.0 6.7 - - + -
947F ASN 2.7 20.1 + - - +
948F VAL* 3.8 9.6 - - - +
949F ILE 3.3 0.2 - - - -
950F PRO* 1.3 72.1 - - - +
952F ILE* 1.3 59.2 + - - +
954F LYS* 3.4 6.4 + - - +
955F LEU* 2.9 29.3 + - - +
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Residues in contact with ILE 952 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948F VAL 3.0 18.5 + - - +
949F ILE* 3.7 7.9 - - - +
951F ASP* 1.3 75.3 - - - +
953F LEU* 1.3 58.7 + - - +
955F LEU* 3.3 6.4 + - - +
956F ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 953 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949F ILE 2.9 16.5 + - - +
950F PRO* 3.7 8.3 - - + +
951F ASP 3.3 0.2 - - - -
952F ILE* 1.3 77.9 - - - +
954F LYS* 1.3 56.6 + - - +
956F ALA* 3.4 6.6 + - - +
957F LYS* 2.9 31.1 + - - +
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Residues in contact with LYS 954 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905F LEU* 5.4 12.3 - - + -
950F PRO 2.9 17.2 + - - +
951F ASP* 3.8 7.0 - - - +
953F LEU* 1.3 75.0 - - - +
955F LEU* 1.3 59.1 + - - +
957F LYS* 4.4 4.9 - - - +
958F GLN* 2.8 37.5 + - + +
961F VAL* 6.5 1.1 - - + -
962F LEU* 4.0 8.5 - - + +
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Residues in contact with LEU 955 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951F ASP 2.9 17.6 + - - +
952F ILE* 3.7 8.1 - - - +
953F LEU 3.3 0.2 - - - -
954F LYS* 1.3 78.0 - - - +
956F ALA* 1.3 58.9 + - - +
958F GLN 3.1 12.8 - - - +
962F LEU* 3.7 19.2 - - + +
996F SER* 4.6 11.1 - - - +
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Residues in contact with ALA 956 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952F ILE 2.9 17.6 + - - +
953F LEU* 3.9 6.5 - - - +
955F LEU* 1.3 76.8 - - - +
957F LYS* 1.3 60.0 + - - +
996F SER* 4.5 17.9 - - - -
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Residues in contact with LYS 957 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953F LEU 2.9 18.1 + - - +
954F LYS* 4.2 2.7 - - - +
956F ALA* 1.3 80.2 - - - +
958F GLN* 1.3 62.2 + - + +
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Residues in contact with GLN 958 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954F LYS* 2.8 27.1 + - + +
955F LEU 3.1 16.6 - - - +
957F LYS* 1.3 78.1 - - + +
959F CYS* 1.3 63.0 + - - +
960F GLU 4.8 3.1 - - - +
961F VAL* 4.8 16.2 - - + +
962F LEU* 3.8 7.2 - - - +
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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
------------------------------------------------------------
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