Contacts of the helix formed by residues 937 - 950 (chain I) in PDB entry 4XLN
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 ASP 937 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G GLN* 3.4 21.3 - - + +
181G VAL* 2.7 34.0 + - - +
935I GLY 3.3 3.8 + - - -
936I VAL* 1.3 76.2 - - - +
938I LYS* 1.3 77.2 + - - +
939I ARG* 2.5 34.7 + - - +
940I GLU* 3.2 31.5 + - + +
941I LYS* 3.1 21.5 + - - +
975I TYR* 2.8 18.0 + - - +
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Residues in contact with LYS 938 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ARG* 4.1 14.2 - - - +
31G GLY* 4.4 4.2 - - - +
181G VAL* 3.3 21.9 + - + +
182G GLU* 5.0 3.8 - - - +
183G ASP* 4.2 19.6 + - - +
191G ASP* 3.2 30.4 + - - +
192G LEU 4.0 1.8 + - - +
193G ASP* 3.0 34.5 + - - +
936I VAL 3.8 0.8 + - - -
937I ASP* 1.3 79.7 + - - +
939I ARG* 1.3 56.2 + - + +
941I LYS* 3.3 14.7 + - + +
942I GLU* 2.9 25.6 + - - +
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Residues in contact with ARG 939 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G VAL* 4.0 19.3 - - + -
179G PHE* 2.6 53.6 + - - -
180G GLN* 3.5 12.9 - - - +
181G VAL* 4.4 5.9 - - + +
860I HIS* 5.3 0.8 + - - -
937I ASP* 2.5 27.5 + - - +
938I LYS* 1.3 76.5 - - + +
940I GLU* 1.3 64.8 + - - +
942I GLU* 3.0 15.8 + - - +
943I VAL* 2.9 26.9 + - - +
975I TYR* 3.3 36.9 - - + +
980I GLY 3.1 28.2 + - - -
982I PRO* 3.5 24.2 - - + -
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Residues in contact with GLU 940 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862I PRO* 3.6 3.5 - - - +
929I ARG* 3.1 35.0 + - - -
936I VAL* 3.4 18.4 - - + +
937I ASP* 3.2 27.8 + - + +
939I ARG* 1.3 77.4 - - - +
941I LYS* 1.3 55.8 + - - +
943I VAL* 3.3 2.6 + - - +
944I LEU* 2.9 35.4 + - - +
963I LEU* 3.5 24.5 - - + +
973I VAL* 3.9 25.8 - - + +
975I TYR* 3.2 24.8 + - - +
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Residues in contact with LYS 941 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G ASP* 4.6 12.5 + - - -
936I VAL* 3.6 29.0 + - + +
937I ASP 3.1 14.6 + - - +
938I LYS* 3.3 15.5 - - + +
940I GLU* 1.3 75.9 - - - +
942I GLU* 1.3 59.5 + - - +
944I LEU* 3.2 6.1 + - + +
945I ALA* 2.9 32.2 + - - +
959I PRO* 3.6 33.9 - - + -
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Residues in contact with GLU 942 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938I LYS 2.9 13.5 + - - +
939I ARG* 3.1 16.1 - - - +
941I LYS* 1.3 77.4 - - - +
943I VAL* 1.3 58.6 + - + +
945I ALA* 3.8 10.1 - - - +
946I ARG* 3.3 22.1 - - - +
981I GLU* 5.3 4.9 - - - +
982I PRO* 3.9 29.0 - - + +
984I GLU* 5.7 6.9 - - - +
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Residues in contact with VAL 943 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939I ARG 2.9 14.8 + - - +
940I GLU 3.8 4.9 - - - +
942I GLU* 1.3 76.5 - - + +
944I LEU* 1.3 60.9 + - + +
945I ALA 3.2 0.6 + - - -
946I ARG* 3.3 9.5 - - - +
947I ALA* 2.9 27.4 + - + +
966I LEU* 5.9 2.5 - - + -
973I VAL* 4.2 22.2 - - + -
974I LEU 5.6 0.4 - - - +
982I PRO* 3.8 18.2 - - + -
983I PHE 3.4 26.7 - - - +
984I GLU* 5.2 0.4 - - - -
985I GLY* 4.0 24.5 - - - +
986I PRO* 4.0 11.4 - - + -
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Residues in contact with LEU 944 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936I VAL* 4.8 2.5 - - + -
940I GLU* 2.9 27.6 + - - +
941I LYS* 3.7 7.9 - - + +
943I VAL* 1.3 75.9 - - + +
945I ALA* 1.3 61.4 + - - +
947I ALA* 3.7 3.6 - - - +
948I GLU* 2.9 30.0 + - - +
953I VAL* 4.3 4.8 - - + +
959I PRO* 3.7 42.0 - - + +
962I GLN* 3.7 24.6 - - + +
963I LEU* 3.7 38.6 - - + +
966I LEU* 4.9 15.3 - - + -
973I VAL* 5.6 2.2 - - + -
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Residues in contact with ALA 945 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941I LYS 2.9 16.2 + - - +
942I GLU* 3.8 8.3 - - - +
944I LEU* 1.3 77.0 - - - +
946I ARG* 1.3 59.4 + - + +
948I GLU* 2.9 24.5 + - - +
949I LYS* 2.9 20.9 + - + +
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Residues in contact with ARG 946 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942I GLU* 3.3 22.2 - - - +
943I VAL* 3.3 16.2 - - - +
945I ALA* 1.3 73.3 - - - +
947I ALA* 1.3 64.0 + - - +
949I LYS* 3.8 15.3 - - - +
950I LEU* 3.1 31.9 + - + +
984I GLU* 2.8 62.0 + - - +
985I GLY* 5.5 0.2 - - - -
791J TYR* 3.3 15.8 + - - -
796J ARG* 4.3 5.5 - - - +
859J ASP* 2.8 37.7 + - - -
861J GLN* 3.4 20.8 + - - +
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Residues in contact with ALA 947 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943I VAL* 2.9 20.3 + - + +
944I LEU* 3.7 10.3 - - - +
946I ARG* 1.3 78.1 - - - +
948I GLU* 1.3 58.4 + - - +
950I LEU* 3.6 11.4 - - - +
951I GLY 3.5 1.9 + - - -
952I LEU* 2.9 38.5 + - + +
953I VAL* 3.5 8.0 + - + -
966I LEU* 4.2 25.4 - - + -
986I PRO* 4.8 7.4 - - + -
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Residues in contact with GLU 948 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944I LEU 2.9 14.6 + - - +
945I ALA* 3.2 11.6 - - - +
947I ALA* 1.3 76.8 - - - +
949I LYS* 1.3 65.0 + - + +
951I GLY* 3.2 13.5 + - - -
953I VAL* 3.7 17.0 - - + +
955I PRO* 3.2 41.7 - - + +
956I GLY 3.7 4.6 + - - -
957I LYS 4.8 0.2 - - - +
962I GLN* 2.4 31.7 + - - +
798J GLU* 4.8 0.7 - - - +
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Residues in contact with LYS 949 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945I ALA* 2.9 19.4 + - + +
946I ARG* 3.3 15.5 + - - +
948I GLU* 1.3 84.0 - - + +
950I LEU* 1.3 59.3 + - - +
951I GLY 3.4 0.5 + - - -
796J ARG* 3.0 46.6 - - - +
798J GLU* 3.1 49.1 + - - +
823J LEU* 4.0 20.7 - - + +
859J ASP* 3.4 10.1 + - - -
862J ASP* 3.9 5.7 + - - -
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Residues in contact with LEU 950 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946I ARG* 3.1 25.3 + - + +
947I ALA* 3.6 15.9 - - + +
949I LYS* 1.3 76.5 - - - +
951I GLY* 1.3 57.5 + - - +
952I LEU* 3.6 32.8 - - + +
984I GLU 6.1 0.4 - - - +
986I PRO* 5.5 6.1 - - + -
796J ARG* 6.0 4.9 - - - +
1014J ASN 4.8 8.7 - - - +
1015J TYR* 4.9 12.1 - - + -
1016J PRO* 5.7 1.7 - - - +
1017J PHE* 4.4 36.1 - - + +
1018J ASN* 6.4 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