Contacts of the helix formed by residues 980 - 1001 (chain B) in PDB entry 4UN5
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 980 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 4.5 6.7 - - + +
52B LEU* 3.8 32.8 - - + +
979B ASN* 1.3 80.3 + - - +
981B TYR* 1.3 68.1 + - + +
982B HIS* 3.2 11.5 + - - -
983B HIS* 3.6 33.9 + - - +
984B ALA* 4.5 1.4 + - - +
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Residues in contact with TYR 981 (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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979B ASN* 3.3 35.4 + - + +
980B ASN* 1.3 83.1 - - + +
982B HIS* 1.3 56.9 + - - +
984B ALA* 3.2 10.7 + - + +
985B HIS* 2.9 55.5 + + + +
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Residues in contact with HIS 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B ARG* 4.2 5.1 + - - +
974B LYS* 4.2 28.3 - - + -
975B VAL 4.8 3.3 + - - +
976B ARG* 3.6 45.5 + - + +
979B ASN* 3.0 29.2 + - - +
980B ASN* 4.1 6.7 - - - -
981B TYR* 1.3 78.4 - - - +
983B HIS* 1.3 92.6 + + - +
985B HIS* 3.9 10.8 + - - +
986B ASP* 2.9 36.8 + - - +
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Residues in contact with HIS 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 4.1 6.4 - - + +
15B SER* 3.4 31.6 + - - +
17B GLY* 3.9 12.6 - - - +
50B ALA* 3.9 15.0 - - + -
52B LEU* 3.9 20.1 - - + +
980B ASN* 3.6 20.7 + - - +
981B TYR 3.2 0.6 - - - -
982B HIS* 1.3 109.1 + + - +
984B ALA* 1.3 58.3 + - - +
986B ASP* 3.2 10.5 + - - +
987B ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP 4.5 0.2 - - - -
48B ILE* 3.8 22.7 - - + +
49B GLY* 3.3 37.5 - - - +
50B ALA* 4.1 3.8 - - + +
981B TYR* 3.2 12.3 + - + +
983B HIS* 1.3 74.6 - - - +
985B HIS* 1.3 68.0 + - + +
987B ALA* 3.0 8.4 + - - +
988B TYR* 2.9 22.0 + - - +
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Residues in contact with HIS 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 4.3 15.5 - - + -
967B ARG* 4.3 17.8 + - - +
981B TYR* 2.9 49.4 + + + +
982B HIS* 3.9 8.4 - - - +
984B ALA* 1.3 76.5 - - + +
986B ASP* 1.3 57.8 + - - +
988B TYR* 3.2 8.8 + + + +
989B LEU* 2.9 38.9 + - + +
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Residues in contact with ASP 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 4.4 10.1 - - + -
762B GLU* 5.0 4.5 - - - +
963B VAL* 4.1 12.5 - - + +
967B ARG* 2.4 31.0 + - - +
974B LYS* 2.9 26.2 + - - -
982B HIS* 2.9 27.0 + - - +
983B HIS* 3.3 10.9 - - - +
985B HIS* 1.3 76.6 - - - +
987B ALA* 1.3 56.0 + - - +
989B LEU* 3.4 4.0 + - - +
990B ASN* 2.9 36.8 + - - +
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Residues in contact with ALA 987 (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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8B GLY* 3.4 24.3 - - - +
9B LEU 4.0 0.9 - - - +
10B ALA* 4.0 3.1 - - - +
17B GLY 3.4 35.9 - - - +
18B TRP* 3.5 5.8 - - - +
19B ALA* 4.2 1.8 - - - -
983B HIS 3.0 8.3 + - - +
984B ALA 3.0 7.8 + - - +
986B ASP* 1.3 74.5 - - - +
988B TYR* 1.3 63.6 + - - +
990B ASN* 3.2 14.4 + - - +
991B ALA 3.0 18.0 + - - -
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Residues in contact with TYR 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA* 3.6 17.8 - - + +
21B ILE* 3.6 20.0 - - + -
25B TYR* 2.8 30.6 + - - +
27B VAL* 4.5 20.4 - - + -
48B ILE* 4.1 11.4 - - + -
984B ALA 2.9 12.0 + - - +
985B HIS* 3.5 10.3 - + + +
987B ALA* 1.3 76.9 - - - +
989B LEU* 1.3 83.6 + - + +
991B ALA* 3.0 6.8 + - - +
992B VAL* 3.0 43.7 + - + +
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Residues in contact with LEU 989 (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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963B VAL* 3.8 15.5 - - + -
966B PHE* 4.4 22.2 - - + -
967B ARG* 3.6 52.3 - - + +
972B PHE* 5.2 12.1 - - + -
985B HIS* 2.9 20.6 + - + +
986B ASP 3.8 3.8 - - - +
988B TYR* 1.3 94.9 - - + +
990B ASN* 1.3 57.3 + - - +
992B VAL* 4.5 5.4 - - + -
993B VAL* 2.9 38.7 + - + +
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Residues in contact with ASN 990 (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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9B LEU 3.5 24.6 + - - +
10B ALA* 4.0 2.0 - - - +
760B VAL* 3.4 24.9 - - + +
762B GLU* 3.5 36.5 + - + +
958B LEU* 3.9 6.8 - - - +
959B LYS 5.6 0.7 - - - +
960B SER* 6.0 0.2 - - - -
963B VAL* 3.2 24.7 - - - +
986B ASP* 2.9 30.4 + - - +
987B ALA* 3.2 10.2 - - - +
989B LEU* 1.3 76.9 - - - +
991B ALA* 1.3 63.0 + - - +
994B GLY* 2.9 19.9 + - - -
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Residues in contact with ALA 991 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER* 5.2 1.1 - - - -
7B ILE 4.1 3.4 - - - +
8B GLY* 3.7 26.4 - - - +
19B ALA 5.1 0.4 - - - +
21B ILE* 3.7 29.2 - - + -
760B VAL* 4.0 11.9 - - + -
987B ALA 3.0 6.4 + - - +
988B TYR* 3.4 9.2 - - - +
990B ASN* 1.3 76.0 - - - +
992B VAL* 1.3 55.7 + - - +
994B GLY* 3.9 0.2 - - - -
995B THR* 2.8 39.4 + - - +
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Residues in contact with VAL 992 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.3 4.3 - - + -
25B TYR* 3.7 34.0 - - + -
966B PHE* 5.4 8.7 - - + -
988B TYR* 3.0 56.8 + - + +
989B LEU* 3.9 7.2 - - + +
991B ALA* 1.3 74.9 - - - +
993B VAL* 1.3 70.4 + - + +
995B THR* 3.0 7.3 + - - -
996B ALA* 2.9 28.6 + - + +
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Residues in contact with VAL 993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B LEU* 4.7 9.6 - - + -
962B LEU* 4.8 12.1 - - + -
963B VAL* 4.3 11.2 - - + -
966B PHE* 3.8 41.3 - - + -
989B LEU* 2.9 25.2 + - + +
990B ASN 4.4 0.7 - - - +
992B VAL* 1.3 78.0 - - + +
994B GLY* 1.3 58.9 + - - +
996B ALA* 3.8 5.5 - - - +
997B LEU* 2.9 31.9 + - + +
1043B MET* 3.7 28.5 - - + -
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Residues in contact with GLY 994 (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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760B VAL* 4.3 7.0 - - - -
956B ILE* 4.3 8.3 - - - -
958B LEU* 3.8 20.8 - - - +
990B ASN 2.9 18.3 + - - -
991B ALA 3.9 0.2 - - - -
993B VAL* 1.3 73.7 - - - +
995B THR* 1.3 64.5 + - - +
997B LEU* 3.1 7.3 + - - +
998B ILE* 3.0 26.9 + - - +
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Residues in contact with THR 995 (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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6B SER* 3.9 20.6 - - - +
21B ILE* 4.0 5.8 - - + +
25B TYR* 3.5 14.2 - - - -
758B ASN* 3.5 32.5 - - + +
760B VAL* 4.5 5.5 - - + +
956B ILE* 4.8 0.4 - - - -
991B ALA 2.8 25.9 + - - +
992B VAL* 3.0 10.2 + - - -
994B GLY* 1.3 72.5 - - - +
996B ALA* 1.3 55.5 + - - +
998B ILE* 3.5 8.3 + - - +
999B LYS* 2.9 45.4 + - - +
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Residues in contact with ALA 996 (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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25B TYR* 3.8 22.4 + - + +
992B VAL* 2.9 21.6 + - + +
993B VAL* 3.8 5.6 - - - +
995B THR* 1.3 77.4 + - - +
997B LEU* 1.3 58.4 + - - +
999B LYS* 3.3 4.5 + - - +
1000B LYS* 2.9 32.3 + - - +
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Residues in contact with LEU 997 (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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958B LEU* 4.7 8.7 - - + -
962B LEU* 4.1 22.7 - - + -
993B VAL* 2.9 23.0 + - + +
994B GLY* 3.1 5.6 + - - +
996B ALA* 1.3 76.5 - - - +
998B ILE* 1.3 64.0 + - + +
1000B LYS* 3.3 5.8 + - - +
1001B TYR* 3.0 31.2 + - + +
1004B LEU* 3.8 28.7 - - + -
1008B PHE* 4.5 20.6 - - + -
1042B ILE* 4.8 8.3 - - + +
1043B MET* 4.0 27.6 - - + -
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Residues in contact with ILE 998 (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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758B ASN* 4.2 5.6 - - - +
954B LYS* 3.6 36.6 - - + +
956B ILE* 3.6 38.4 - - + -
994B GLY 3.0 12.9 + - - +
995B THR* 3.6 10.3 - - - +
997B LEU* 1.3 81.1 - - + +
999B LYS* 1.3 69.8 + - + +
1001B TYR 4.0 7.9 - - - +
1002B PRO* 3.4 25.6 - - - +
1004B LEU* 5.7 1.3 - - + +
1005B GLU* 4.8 15.6 - - + +
1008B PHE* 4.7 10.5 - - + -
1009B VAL* 4.6 13.0 - - + -
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Residues in contact with LYS 999 (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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23B ASP* 4.4 15.8 + - - -
24B GLU* 5.4 1.6 + - - -
25B TYR* 2.9 31.2 + - - -
758B ASN* 5.9 3.6 - - - +
995B THR* 2.9 34.0 + - - +
996B ALA* 3.7 4.3 - - - +
997B LEU 3.3 0.2 - - - -
998B ILE* 1.3 80.9 - - + +
1000B LYS* 1.3 61.7 + - - +
1002B PRO* 4.2 8.9 - - - +
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Residues in contact with LYS1000 (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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996B ALA 2.9 17.1 + - - +
997B LEU* 3.7 5.2 - - - +
999B LYS* 1.3 79.1 - - - +
1001B TYR* 1.3 105.3 + - + +
1002B PRO* 3.3 8.3 - - - +
1045B PHE* 5.5 11.2 - - - +
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Residues in contact with TYR1001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B LEU* 3.0 17.3 + - + +
998B ILE* 3.4 9.7 - - - +
1000B LYS* 1.3 118.9 - - + +
1002B PRO* 1.3 62.3 - - - +
1003B LYS* 3.1 8.3 - - + +
1004B LEU* 3.1 35.7 + - + +
1005B GLU 4.4 1.0 + - - -
1038B PHE* 5.5 9.6 - + + -
1041B ASN 5.3 2.3 + - - -
1042B ILE* 3.5 49.4 + - + -
1045B PHE* 5.2 7.8 + - - -
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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