Contacts of the strand formed by residues 961 - 972 (chain B) in PDB entry 3HOU
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 LEU 961 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862B GLN* 5.0 4.9 - - - +
863B GLU* 2.9 30.7 - - + +
864B LYS* 4.6 0.9 - - - -
865B LYS* 3.5 43.1 - - + +
871B THR* 4.5 10.5 - - + -
956B THR* 3.0 27.5 - - - -
957B ASN* 2.9 22.8 + - - +
959B ASP* 3.2 28.4 + - + +
960B GLY* 1.3 82.3 - - - +
962B LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B GLN* 3.1 26.4 - - - +
863B GLU* 2.9 41.9 + - + +
874B PHE* 3.9 20.8 - - + -
954B VAL* 4.2 20.6 - - + -
955B THR 3.9 2.5 - - - +
956B THR* 4.9 2.0 - - - +
960B GLY 4.2 0.2 + - - -
961B LEU* 1.3 71.9 - - - +
963B PHE* 1.3 59.8 + - - +
41L SER 4.7 3.6 + - - -
42L ARG* 4.1 28.3 - - - +
43L THR 4.3 5.7 - - - +
44L ASP 5.8 0.4 - - - +
45L ALA 5.6 2.4 + - - -
46L VAL* 5.1 15.3 - - + -
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Residues in contact with PHE 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU 3.4 18.6 - - - -
120B ARG* 3.3 28.0 - - - -
121B ASN* 3.3 27.8 - - + -
860B MET* 3.4 28.0 - - + -
861B ASP 3.7 1.3 - - - -
862B GLN* 3.1 35.0 - - + -
953B LEU* 3.8 1.7 - - + +
954B VAL* 3.3 5.7 - - - +
955B THR* 2.6 56.1 + - - +
956B THR 4.0 15.5 - - - +
957B ASN* 4.5 4.0 - - + -
961B LEU 3.3 0.9 + - - +
962B LYS* 1.3 74.2 - - - +
964B VAL* 1.3 66.9 + - - +
965B LYS* 3.8 15.0 - - + -
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Residues in contact with VAL 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B MET* 3.2 6.2 - - - +
861B ASP 2.9 36.8 + - - +
874B PHE* 3.4 37.0 - - + -
898B LEU* 3.9 32.1 - - + -
912B ILE* 3.8 18.6 - - + -
952B VAL* 4.0 7.0 - - + -
953B LEU* 3.0 22.7 - - - +
954B VAL* 4.4 5.2 - - + -
963B PHE* 1.3 78.8 - - - +
965B LYS* 1.3 65.7 + - - +
966B VAL* 4.8 1.1 - - + -
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Residues in contact with LYS 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG 3.7 5.3 + - - -
119B LEU* 3.3 22.6 + - - +
121B ASN* 3.1 31.7 - - - +
789B MET* 2.9 58.4 + - + +
858B SER* 5.4 2.2 - - - +
859B TYR 3.4 6.7 - - - +
860B MET* 3.4 29.6 - - + +
952B VAL* 3.5 0.5 - - - -
953B LEU* 3.0 34.0 + - + +
963B PHE* 3.8 11.7 - - + -
964B VAL* 1.3 75.8 - - - +
966B VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B MET* 4.3 0.2 - - - -
857B ARG 3.8 0.2 - - - +
858B SER* 3.2 6.8 - - - -
859B TYR* 3.0 34.9 + - + +
898B LEU* 4.6 4.0 - - + -
899B ILE* 5.6 0.7 - - + +
911B ILE* 3.2 40.6 - - + +
912B ILE* 3.7 26.9 - - + -
949B VAL* 4.0 24.5 - - + -
951B GLN 3.8 2.7 - - - -
952B VAL* 4.1 18.4 - - + +
964B VAL* 4.8 0.2 - - + -
965B LYS* 1.3 75.9 - - - +
967B ARG* 1.3 69.3 + - - +
968B VAL* 4.2 2.2 - - + +
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Residues in contact with ARG 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B TYR 4.5 2.4 + - - -
786B ASN* 3.2 40.9 + - - +
787B VAL 4.6 1.0 - - - -
788B ARG 3.1 26.2 + - - +
789B MET* 3.9 18.2 - - - -
790B ASP* 6.0 0.4 - - - -
856B PHE* 3.4 35.1 - - + -
857B ARG 3.3 12.1 - - - +
858B SER* 3.9 11.2 - - - +
950B ASP* 2.7 66.0 + - - +
951B GLN* 3.0 39.1 + - - +
966B VAL* 1.3 81.7 - - - +
968B VAL* 1.3 53.4 + - - +
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Residues in contact with VAL 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B PHE* 3.9 1.2 - - - +
856B PHE* 3.5 2.3 - - - -
857B ARG* 3.1 34.4 + - + +
859B TYR* 4.0 8.3 - - + -
905B VAL* 4.1 9.2 - - + -
911B ILE* 3.9 14.1 - - + -
941B LEU* 3.4 29.4 - - + -
946B ASN 4.5 1.6 - - - -
947B GLY* 3.6 17.7 - - - +
948B ILE 3.4 28.9 - - - +
949B VAL* 4.5 8.7 - - + -
950B ASP* 4.1 1.1 - - - +
966B VAL* 4.2 2.4 - - + -
967B ARG* 1.3 74.2 - - - +
969B ARG* 1.3 63.9 + - - +
970B THR* 4.5 2.4 + - - +
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Residues in contact with ARG 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854B LEU* 4.4 6.5 - - + -
855B PHE 3.5 4.9 - - - +
856B PHE* 3.6 29.8 - - + -
901B PRO 5.3 1.4 + - - -
947B GLY* 3.6 0.5 - - - -
948B ILE* 2.9 72.6 + - - +
949B VAL 4.5 0.2 + - - -
950B ASP* 3.2 36.6 + - + +
967B ARG 3.8 0.4 + - - -
968B VAL* 1.3 73.3 - - - +
970B THR* 1.3 70.8 + - - +
59C ALA* 3.9 16.1 - - - +
60C ASP* 3.2 21.9 + - - -
61C GLU* 2.4 56.3 + - - +
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Residues in contact with THR 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B LEU* 3.5 2.9 - - - -
855B PHE* 2.8 54.2 + - - +
945B GLU* 5.9 1.4 - - - +
946B ASN* 2.9 30.8 + - - +
947B GLY* 3.6 3.8 - - - -
968B VAL* 4.5 2.9 - - - +
969B ARG* 1.3 79.3 + - - +
971B THR* 1.3 78.0 + - - +
972B LYS* 4.2 13.0 - - + -
61C GLU* 4.3 3.4 - - - -
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Residues in contact with THR 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B TYR* 2.8 34.4 + - + +
852B ARG* 4.6 7.6 - - - +
853B SER 3.4 11.9 - - - +
854B LEU* 3.3 8.7 - - - +
970B THR* 1.3 85.2 - - - +
972B LYS* 1.3 68.0 + - - +
973B ILE* 4.0 15.2 + - + +
61C GLU* 3.0 25.8 + - - +
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Residues in contact with LYS 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B ASN* 5.2 2.6 + - - +
853B SER* 3.0 29.4 + - - +
855B PHE* 3.6 51.4 - - + -
945B GLU* 5.7 3.4 + - - +
970B THR* 3.9 12.5 + - + -
971B THR* 1.3 76.4 - - - +
973B ILE* 1.3 63.4 + - - +
1094B ARG* 3.0 30.6 + - - +
1098B MET* 4.1 23.6 - - + +
1101B ASP* 3.2 34.1 + - - +
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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