Contacts of the helix formed by residues 944 - 955 (chain D) in PDB entry 6CCV
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 944 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920D PHE* 3.6 5.6 - - - -
941D HIS* 5.5 0.8 + - - -
942D ASP* 3.6 3.6 - - - +
943D LEU* 1.3 79.5 - - - +
945D ASP* 1.3 67.3 + - - +
946D PRO* 3.4 9.4 - - - +
947D ALA* 3.4 7.1 + - - +
948D ILE* 3.4 19.8 + - - +
980D ARG* 3.7 16.6 - - - +
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Residues in contact with ASP 945 (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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701D GLU* 4.5 19.2 + - - +
911D ARG* 4.0 9.0 + - - -
916D GLU* 3.8 14.0 - - - +
920D PHE* 3.2 28.0 - - - -
944D GLY* 1.3 71.6 - - - -
946D PRO* 1.3 70.8 - - + +
948D ILE* 3.3 12.1 + - - +
949D ASP* 3.4 20.5 + - - +
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Residues in contact with PRO 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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701D GLU* 6.2 0.4 - - - +
944D GLY* 3.4 6.5 - - - -
945D ASP* 1.3 95.9 - - + +
947D ALA* 1.3 58.8 + - + +
949D ASP* 3.1 10.9 + - + +
950D ALA* 2.8 29.2 + - - +
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Residues in contact with ALA 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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937D ILE* 3.5 22.4 - - + +
941D HIS* 4.0 14.6 - - + +
943D LEU* 4.0 12.6 - - + -
944D GLY 3.4 20.4 + - - +
945D ASP 3.3 1.0 - - - -
946D PRO* 1.3 81.9 - - + +
948D ILE* 1.3 57.8 + - - +
950D ALA* 4.3 4.3 - - - -
951D LEU* 2.8 34.1 + - - +
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Residues in contact with ILE 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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900D LEU* 3.8 27.1 - - + +
911D ARG* 3.3 23.8 - - + +
915D VAL* 4.9 4.9 - - + -
919D ALA* 4.4 13.5 - - + -
920D PHE* 3.3 38.6 - - + -
943D LEU* 4.6 15.0 - - + +
944D GLY 3.4 7.6 + - - +
945D ASP 3.3 4.2 + - - +
946D PRO 3.1 0.6 - - - -
947D ALA* 1.3 77.0 - - - +
949D ASP* 1.3 60.9 + - - +
951D LEU* 3.7 8.9 - - + +
952D LEU* 2.8 52.0 + - + +
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Residues in contact with ASP 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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911D ARG* 2.2 37.6 + - - -
945D ASP* 3.4 16.3 + - - +
946D PRO* 3.1 10.1 + - + +
948D ILE* 1.3 73.7 - - - +
950D ALA* 1.3 65.5 + - - +
952D LEU* 3.2 6.8 + - - +
953D ALA* 3.0 22.3 + - - +
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Residues in contact with ALA 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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936D ILE* 3.0 27.2 - - + +
937D ILE* 5.1 4.0 - - + -
946D PRO 2.8 16.8 + - - +
947D ALA* 3.8 7.9 - - - +
949D ASP* 1.3 76.7 - - - +
951D LEU* 1.3 61.5 + - - +
953D ALA* 3.2 19.8 + - - +
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Residues in contact with LEU 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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900D LEU* 4.3 9.6 - - + -
924D LEU* 5.3 0.4 - - + -
928D ALA* 3.6 16.6 - - + -
936D ILE* 3.3 31.8 - - + +
937D ILE* 3.2 28.5 - - + -
943D LEU* 4.0 17.5 - - + -
947D ALA 2.8 17.6 + - - +
948D ILE* 3.7 7.0 - - + +
950D ALA* 1.3 74.7 - - - +
952D LEU* 1.3 62.9 + - - +
954D ALA* 3.1 11.1 + - - +
955D GLY 3.3 1.0 + - - -
956D ILE* 2.9 41.3 - - + +
959D VAL* 4.0 23.6 - - + -
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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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900D LEU* 3.8 20.6 - - + +
901D ALA* 3.7 29.4 - - + -
910D ILE 5.9 3.1 - - - +
911D ARG* 4.1 27.4 - - + +
948D ILE* 2.8 51.7 + - + +
949D ASP* 3.2 6.7 + - - +
951D LEU* 1.3 72.5 - - - +
953D ALA* 1.3 64.4 + - - +
955D GLY* 2.9 15.9 + - - -
956D ILE* 4.1 6.3 - - - +
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Residues in contact with ALA 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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936D ILE* 5.5 0.2 - - + -
949D ASP 3.0 12.6 + - - +
950D ALA* 3.4 13.7 - - - +
951D LEU 3.2 0.2 - - - -
952D LEU* 1.3 77.3 - - - +
954D ALA* 1.3 61.8 + - - +
955D GLY* 3.1 2.3 + - - -
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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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930D ASP* 3.7 39.9 - - + +
931D ALA* 4.8 4.2 + - - +
936D ILE* 3.6 30.5 - - + +
950D ALA 3.4 1.8 + - - -
951D LEU 3.1 7.4 + - - +
953D ALA* 1.3 78.1 - - - +
955D GLY* 1.3 61.8 + - - +
956D ILE* 4.7 3.4 - - + -
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Residues in contact with GLY 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 ALA* 5.9 2.1 + - - +
951D LEU 3.3 0.6 + - - -
952D LEU* 2.9 18.9 + - - -
953D ALA 3.0 1.5 - - - -
954D ALA* 1.3 79.2 - - - +
956D ILE* 1.3 61.4 + - - +
957D THR* 3.8 9.7 + - - +
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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