Contacts of the helix formed by residues 945 - 955 (chain D) in PDB entry 5UH8
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 GLY 945 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702D GLU* 6.0 1.6 - - - -
921D TYR* 4.2 4.5 - - - -
943D ASP* 4.7 3.8 - - - -
944D LEU* 1.3 73.7 - - - +
946D ASP* 1.3 65.5 + - - -
947D PRO* 3.4 5.8 - - - -
948D GLU* 3.2 21.6 + - - +
949D ILE* 3.1 27.9 + - - +
981D ARG* 5.1 7.9 - - - -
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Residues in contact with ASP 946 (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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702D GLU* 5.8 10.3 + - + +
912D ARG* 5.0 0.2 + - - -
921D TYR* 2.7 35.7 + - + -
945D GLY* 1.3 72.7 - - - +
947D PRO* 1.3 70.2 - - + +
949D ILE* 3.5 3.3 + - - +
950D ASP* 3.3 27.6 + - - +
981D ARG* 5.8 0.2 - - - +
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Residues in contact with PRO 947 (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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945D GLY* 3.5 3.8 - - - -
946D ASP* 1.3 95.9 - - + +
948D GLU* 1.3 66.8 + - + +
950D ASP* 3.0 12.0 + - + +
951D ALA* 2.8 28.3 + - - +
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Residues in contact with GLU 948 (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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938D VAL* 4.1 18.1 - - + +
942D GLN* 3.5 28.5 + - - +
943D ASP* 2.8 28.7 - - - +
944D LEU* 4.4 5.2 - - + -
945D GLY* 3.2 25.5 + - - +
947D PRO* 1.3 84.1 - - + +
949D ILE* 1.3 62.0 + - - +
951D ALA* 3.6 8.8 + - - +
952D LEU* 3.3 29.0 + - - +
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Residues in contact with ILE 949 (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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901D LEU* 4.6 26.3 - - + +
912D ARG* 4.2 13.5 - - - +
916D ILE* 4.6 7.9 - - + -
920D ALA* 4.9 3.4 - - + -
921D TYR* 3.8 42.2 - - + +
944D LEU* 3.8 35.7 - - + -
945D GLY 3.1 15.2 + - - +
946D ASP 3.7 6.7 - - - +
947D PRO 3.1 0.2 - - - -
948D GLU* 1.3 77.6 - - - +
950D ASP* 1.3 59.6 + - - +
952D LEU* 3.2 8.8 + - + +
953D LEU* 2.8 29.2 + - + +
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Residues in contact with ASP 950 (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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912D ARG* 4.8 10.7 + - - -
946D ASP* 3.3 23.4 + - - +
947D PRO* 3.0 11.9 + - + +
949D ILE* 1.3 76.7 - - - +
951D ALA* 1.3 60.0 + - - +
953D LEU* 3.6 16.2 - - - +
954D ALA* 3.0 31.9 + - - +
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Residues in contact with ALA 951 (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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937D ILE* 3.6 24.4 - - + +
938D VAL* 5.1 2.2 - - + -
947D PRO 2.8 13.5 + - - +
948D GLU* 3.8 10.8 - - - +
949D ILE 3.2 0.2 - - - -
950D ASP* 1.3 77.6 - - - +
952D LEU* 1.3 59.7 + - - +
954D ALA* 4.7 1.8 - - - +
955D ALA* 3.2 25.5 + - - +
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Residues in contact with LEU 952 (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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901D LEU* 5.1 7.2 - - + -
925D LEU* 5.3 0.2 - - + -
929D ALA* 3.6 28.3 - - + -
937D ILE* 3.6 24.5 - - + -
938D VAL* 4.0 13.5 - - + -
944D LEU* 4.2 17.3 - - + -
948D GLU 3.3 16.4 + - - +
949D ILE* 3.2 13.3 + - + +
951D ALA* 1.3 75.7 - - - +
953D LEU* 1.3 63.5 + - - +
955D ALA* 3.9 0.9 - - - -
956D GLY 3.6 1.2 + - - -
957D ILE* 3.1 51.4 + - + +
960D VAL* 4.0 24.7 - - + -
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Residues in contact with LEU 953 (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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901D LEU* 4.4 13.4 - - + +
902D ALA* 4.3 17.3 - - + -
910D LEU* 3.3 48.6 - - + +
912D ARG* 3.6 40.2 - - + +
916D ILE* 5.4 0.2 - - + -
949D ILE* 2.8 19.0 + - + +
950D ASP* 3.4 15.9 + - - +
951D ALA 3.3 0.2 - - - -
952D LEU* 1.3 78.9 - - - +
954D ALA* 1.3 60.4 + - - +
956D GLY* 3.6 3.3 + - - -
957D ILE 4.9 1.8 - - - +
958D THR* 6.2 0.2 - - + -
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Residues in contact with ALA 954 (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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950D ASP 3.0 17.0 + - - +
951D ALA* 4.7 2.2 - - - +
953D LEU* 1.3 73.2 - - - +
955D ALA* 1.3 65.0 + - - +
956D GLY* 3.1 2.7 + - - -
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Residues in contact with ALA 955 (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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931D ASP* 3.9 23.4 - - + +
932D GLU 5.3 0.3 + - - -
937D ILE* 4.0 27.1 - - + -
951D ALA 3.2 20.3 + - - +
952D LEU* 4.0 6.7 - - - +
953D LEU 3.3 0.4 - - - -
954D ALA* 1.3 78.6 - - - +
956D GLY* 1.3 56.9 + - - +
957D ILE* 3.4 5.9 + - + -
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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