Contacts of the helix formed by residues 976 - 980 (chain D) in PDB entry 5UH6
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 ALA 976 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886D VAL* 3.9 13.7 - - + -
888D GLU 3.1 21.4 + - - +
889D HIS* 3.5 14.0 + - + +
975D CYS* 1.3 74.1 - - - +
977D THR* 1.3 67.4 + - - +
979D TYR* 3.2 8.0 + - - +
980D GLY 3.2 17.2 + - - -
988D LEU* 4.0 13.4 - - + +
989D VAL* 3.7 26.3 - - + +
991D ILE* 4.7 4.7 - - + -
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Residues in contact with THR 977 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889D HIS* 2.7 24.7 + - - -
890D ASP* 2.7 26.8 + - - +
924D THR* 2.6 37.9 + - + +
925D LEU 5.7 0.2 - - - +
941D GLY* 5.3 9.4 - - - -
963D ARG* 3.4 32.5 - - - +
975D CYS* 3.2 2.3 - - - -
976D ALA* 1.3 76.6 - - - +
978D CYS* 1.3 57.7 + - - +
980D GLY* 3.3 10.0 + - - -
988D LEU* 4.4 9.6 - - + +
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Residues in contact with CYS 978 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923D ARG* 5.4 2.4 + - - -
924D THR* 4.2 4.3 + - - -
963D ARG* 3.2 34.1 - - + +
964D SER* 3.5 19.3 + - - +
965D VAL* 4.8 2.4 + - - -
968D CYS* 2.9 28.0 - - + -
974D VAL* 4.8 5.2 - - - -
975D CYS* 2.0 59.3 - - - -
977D THR* 1.3 71.1 - - - +
979D TYR* 1.3 66.1 + - - +
980D GLY* 3.4 0.5 + - - -
1401D ZN 2.4 16.4 - - - -
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Residues in contact with TYR 979 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886D VAL* 5.2 0.9 - - + -
922D ALA 4.6 0.5 - - - +
923D ARG* 5.3 2.1 - - - -
965D VAL* 4.0 23.1 - - + +
974D VAL* 5.0 4.9 - - + -
975D CYS 3.9 11.0 - - - +
976D ALA 3.2 9.8 + - - +
978D CYS* 1.3 80.2 - - - +
980D GLY* 1.3 56.0 + - - +
982D SER* 4.3 17.4 + - - -
983D MET* 5.4 1.6 + - - +
989D VAL* 3.5 26.7 - - + -
995D VAL* 3.5 48.5 + - + +
998D VAL* 5.6 3.3 - - - +
1152D LYS* 2.5 68.5 + - + +
1153D HIS* 4.0 19.5 + - - -
1156D VAL* 4.5 10.3 - - + -
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Residues in contact with GLY 980 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922D ALA 4.1 3.1 - - - -
924D THR* 3.7 18.2 - - - -
976D ALA 3.2 6.9 + - - -
977D THR 3.6 11.9 - - - -
978D CYS 3.2 2.7 - - - -
979D TYR* 1.3 78.8 - - - +
981D ARG* 1.3 64.7 + - - -
982D SER 3.2 3.6 + - - -
988D LEU* 3.6 9.5 - - - +
989D VAL* 3.3 23.7 + - - +
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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