Contacts of the helix formed by residues 990 - 1001 (chain C) in PDB entry 4UN0
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 PRO 990 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833C GLU* 4.1 35.7 - - + +
930C PHE* 3.9 17.0 - - + -
988C PHE 3.6 7.0 - - - +
989C ILE* 1.3 92.4 - - + +
991C SER* 1.3 60.4 + - - +
992C ALA* 4.5 3.4 - - + +
993C ALA* 3.1 14.8 + - + +
994C LEU* 2.8 26.2 + - - +
1019C PHE* 5.3 0.4 - - + -
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Residues in contact with SER 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983C ARG* 5.7 1.2 + - - +
989C ILE 3.7 1.7 + - - -
990C PRO* 1.3 72.7 - - - +
992C ALA* 1.3 60.9 + - - +
994C LEU* 3.5 5.7 + - - +
995C ASP* 2.8 37.7 + - - +
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Residues in contact with ALA 992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833C GLU* 5.9 1.8 - - - +
837C LYS* 6.0 2.9 - - - +
990C PRO* 3.3 3.5 - - + +
991C SER* 1.3 78.9 - - - +
993C ALA* 1.3 62.0 + - - +
994C LEU 3.6 0.2 + - - -
995C ASP* 3.6 16.7 + - - +
996C LEU* 3.8 3.5 + - - +
1017C SER* 5.8 0.3 - - - -
1018C ASP* 4.0 26.6 + - + +
1019C PHE* 3.5 25.7 + - + +
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Residues in contact with ALA 993 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926C LEU* 4.3 4.9 - - + +
930C PHE* 4.0 11.4 - - + -
989C ILE* 3.5 15.7 - - + +
990C PRO* 3.1 15.7 + - + +
992C ALA* 1.3 79.8 - - - +
994C LEU* 1.3 63.3 + - - +
996C LEU* 3.3 6.2 + - - +
997C LEU* 3.2 19.9 + - - +
1019C PHE* 3.5 39.9 - - + -
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Residues in contact with LEU 994 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982C LEU* 4.0 12.1 - - + -
983C ARG* 3.8 45.5 + - + +
986C PHE* 3.6 41.3 - - + +
987C SER* 5.0 2.2 - - - -
989C ILE* 3.5 11.4 - - + +
990C PRO 2.8 15.6 + - - +
991C SER* 4.0 6.1 - - - +
993C ALA* 1.3 74.6 - - - +
995C ASP* 1.3 60.2 + - - +
997C LEU* 3.8 17.0 - - + -
998C ASP* 2.9 29.3 + - - +
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Residues in contact with ASP 995 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983C ARG* 3.2 29.6 + - - +
991C SER* 2.8 23.3 + - - +
992C ALA* 3.7 12.6 - - - +
993C ALA 3.2 0.6 - - - -
994C LEU* 1.3 78.2 - - - +
996C LEU* 1.3 59.0 - - - +
998C ASP* 3.9 0.2 - - - +
999C HIS* 3.2 41.0 + - + -
1017C SER* 6.2 1.3 - - - -
1018C ASP* 6.0 3.1 - - + +
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Residues in contact with LEU 996 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840C MET* 5.4 2.9 - - + -
926C LEU* 3.6 20.4 - - + -
992C ALA 3.8 7.1 + - - +
993C ALA 3.3 8.6 + - - +
994C LEU 3.2 0.2 - - - -
995C ASP* 1.3 77.2 - - - +
997C LEU* 1.3 59.5 + - - +
998C ASP 3.1 0.2 - - - -
999C HIS* 3.1 4.4 + - - -
1000C MET* 2.9 64.0 + - + +
1009C CYS* 5.3 5.6 - - - -
1014C THR* 3.9 20.4 - - + +
1017C SER* 3.9 21.7 - - - +
1019C PHE* 4.5 7.2 - - + -
1020C LEU* 3.4 28.9 - - + -
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Residues in contact with LEU 997 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923C GLY* 3.3 28.3 - - - +
926C LEU* 3.8 15.9 - - + +
927C GLY* 3.6 14.6 - - - +
935C ILE* 5.5 0.2 - - + -
982C LEU* 4.2 4.6 - - + +
986C PHE* 3.7 43.1 - - + -
989C ILE* 3.7 16.4 - - + -
993C ALA 3.2 13.3 + - - +
994C LEU* 3.4 13.9 + - + +
996C LEU* 1.3 78.8 - - - +
998C ASP* 1.3 60.7 + - - +
1000C MET* 3.7 1.7 + - - -
1001C LEU* 3.3 42.4 + - + +
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Residues in contact with ASP 998 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980C ARG* 2.7 62.5 + - - +
982C LEU* 3.8 18.4 - - + +
983C ARG* 3.2 36.4 + - - +
994C LEU 2.9 18.4 + - - +
995C ASP 3.9 2.5 - - - +
997C LEU* 1.3 78.9 - - - +
999C HIS* 1.3 68.7 + - + +
1001C LEU 3.6 2.1 + - - -
1002C THR* 3.3 7.8 - - - +
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Residues in contact with HIS 999 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983C ARG* 4.5 6.7 + - - -
995C ASP* 3.2 28.0 + - + +
996C LEU* 3.1 6.0 + - - +
998C ASP* 1.3 92.3 + - - +
1000C MET* 1.3 63.6 + - - +
1002C THR* 3.3 24.6 + - + +
1009C CYS* 3.5 42.6 + - - +
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Residues in contact with MET1000 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840C MET* 5.3 4.7 - - - -
844C MET* 4.0 25.6 - - + -
919C VAL* 4.1 16.1 - - + +
920C TRP* 3.9 12.5 - - - -
922C CYS* 4.4 7.2 - - + +
923C GLY* 3.8 31.0 - - - -
926C LEU* 4.0 9.4 - - - -
996C LEU* 2.9 48.6 + - + +
997C LEU 4.1 3.6 - - - +
999C HIS* 1.3 79.9 - - - +
1001C LEU* 1.3 57.8 + - - +
1002C THR 3.3 3.8 + - - -
1008C ARG* 3.5 22.3 - - - -
1009C CYS* 4.7 0.9 - - + -
1014C THR* 3.6 29.8 - - + -
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Residues in contact with LEU1001 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920C TRP* 3.4 46.0 - - + +
923C GLY* 3.9 23.8 - - - +
924C CYS* 4.0 6.3 - - - +
935C ILE* 4.3 13.9 - - + -
936C PHE* 4.9 3.1 - - + -
951C LEU* 5.2 2.5 - - + -
952C CYS* 3.7 12.7 - - - -
980C ARG* 3.1 22.0 + - - -
982C LEU* 3.8 21.8 - - + -
986C PHE* 5.9 1.1 - - + -
997C LEU* 3.3 43.6 + - + +
999C HIS 3.3 0.6 - - - -
1000C MET* 1.3 77.9 - - - +
1002C THR* 1.3 58.4 + - - -
1003C LEU 3.9 0.3 + - - -
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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