Contacts of the helix formed by residues 944 - 953 (chain A) in PDB entry 4K6J
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 944 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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866A PRO 5.2 1.2 + - - -
869A GLN* 4.4 15.3 + - - +
870A SER* 4.3 20.4 + - - +
873A ILE* 3.4 21.3 - - + +
940A LEU 3.4 17.5 - - - +
941A THR* 3.8 7.1 - - - +
942A ASN 4.4 0.2 - - - +
943A ASP* 1.3 77.6 - - - +
945A GLU* 1.3 59.0 + - - +
946A TRP* 3.0 14.3 + - - +
947A GLY 2.9 17.5 + - - -
948A SER* 3.2 20.6 + - - -
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Residues in contact with GLU 945 (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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941A THR 4.5 6.6 - - - +
942A ASN 4.6 1.0 - - - +
943A ASP* 3.6 15.5 + - - +
944A ASN* 1.3 73.0 + - - +
946A TRP* 1.3 62.6 + - - +
947A GLY 3.2 1.1 - - - -
948A SER* 3.6 20.0 + - - -
949A THR* 2.8 33.4 + - - +
990A ASN 4.7 3.6 - - - +
993A GLU* 4.4 6.1 - - - +
994A TYR* 3.3 47.2 + - + +
995A SER* 4.2 8.1 + - - -
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Residues in contact with TRP 946 (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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873A ILE* 4.3 11.7 - - + -
944A ASN* 3.0 9.9 + - - +
945A GLU* 1.3 74.3 - - - +
947A GLY* 1.3 56.6 + - - +
949A THR* 3.7 15.3 - - + -
950A LYS* 2.8 42.0 + - + +
997A ARG* 5.9 1.1 - - - -
738B ARG* 3.7 51.1 - - + -
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Residues in contact with GLY 947 (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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873A ILE* 3.6 21.4 - - - +
881A ILE* 4.0 4.2 - - - +
940A LEU 3.5 17.9 - - - -
941A THR* 3.7 6.5 - - - -
944A ASN* 2.9 10.7 + - - -
945A GLU 3.2 0.4 - - - -
946A TRP* 1.3 77.1 - - - +
948A SER* 1.3 54.1 + - - +
950A LYS* 3.9 0.5 - - - +
951A THR* 2.7 37.6 + - - -
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Residues in contact with SER 948 (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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941A THR* 3.7 20.3 - - - +
944A ASN 3.2 12.4 + - - -
945A GLU* 3.6 25.2 + - - -
946A TRP 3.3 0.2 - - - -
947A GLY* 1.3 72.8 - - - +
949A THR* 1.3 60.7 + - - +
952A GLY 3.0 23.7 + - - -
990A ASN 3.6 8.6 + - - -
991A LEU* 3.2 19.6 + - - +
995A SER* 4.2 1.6 - - - -
998A ASN* 3.0 26.3 + - - -
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Residues in contact with THR 949 (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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945A GLU* 2.8 23.8 + - - +
946A TRP* 3.7 22.5 - - + -
948A SER* 1.3 77.8 + - - +
950A LYS* 1.3 63.8 + - - +
952A GLY* 3.4 1.0 + - - -
953A GLU* 3.1 50.2 + - + +
995A SER* 4.7 11.4 + - - +
997A ARG* 4.2 14.5 + - - +
998A ASN* 4.4 7.1 - - - +
738B ARG* 4.1 10.3 - - - +
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Residues in contact with LYS 950 (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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873A ILE* 4.8 3.4 - - + -
877A ASP* 4.8 6.4 - - - +
878A SER* 3.3 37.9 - - - +
881A ILE* 3.9 10.0 - - + +
882A VAL* 5.8 1.8 - - - -
946A TRP* 2.8 26.5 + - + +
947A GLY* 4.0 2.2 - - - +
949A THR* 1.3 75.0 - - - +
951A THR* 1.3 60.9 + - - +
953A GLU* 3.5 20.1 + - - +
954A GLN* 3.0 38.5 + - - +
738B ARG* 3.6 25.8 - - - +
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Residues in contact with THR 951 (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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881A ILE* 3.4 28.6 - - + +
937A LEU* 4.2 22.1 - - + +
940A LEU* 5.2 0.2 - - - +
941A THR* 3.4 14.1 - - + +
947A GLY 2.7 23.7 + - - -
950A LYS* 1.3 77.4 - - - +
952A GLY* 1.3 62.0 + - - +
954A GLN* 3.3 15.1 + - - +
957A LEU* 3.2 34.2 - - + +
987A LEU* 4.9 1.3 - - + -
991A LEU* 3.7 17.9 - - + -
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Residues in contact with GLY 952 (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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948A SER 3.0 12.7 + - - -
949A THR 3.9 0.2 - - - -
951A THR* 1.3 77.9 - - - +
953A GLU* 1.3 60.9 + - - +
954A GLN 3.3 6.5 + - - +
957A LEU* 4.7 0.4 - - - -
958A ILE* 3.8 25.5 + - - +
991A LEU* 4.2 5.6 - - - -
998A ASN* 3.3 27.8 - - - -
1001A CYS* 5.2 3.1 - - - -
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Residues in contact with GLU 953 (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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949A THR* 3.1 26.6 + - + +
950A LYS* 3.8 20.9 + - - +
951A THR 3.2 0.8 - - - -
952A GLY* 1.3 75.0 - - - +
954A GLN* 1.3 70.4 + - - +
955A ASP* 3.2 10.6 + - - +
997A ARG* 4.4 7.1 + - - +
998A ASN* 5.6 1.1 - - - +
738B ARG* 2.8 43.1 + - - -
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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