Contacts of the helix formed by residues 961 - 969 (chain D) in PDB entry 6GHM
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 THR 961 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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931D LEU* 3.4 8.5 - - - +
952D PRO 5.0 0.4 - - - -
953D SER* 3.5 30.1 - - - +
954D LEU 4.5 2.2 - - - -
955D PRO* 3.8 15.5 - - + -
959D GLY 3.9 2.7 - - - +
960D ILE* 1.3 81.6 - - - +
962D ALA* 1.3 65.7 + - - +
963D LEU* 3.4 10.1 + - - +
964D HIS* 2.7 43.9 + - - +
965D ASN* 3.2 10.6 + - - -
984D ASN 5.4 0.5 + - - -
987D ALA* 3.9 20.7 - - + +
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Residues in contact with ALA 962 (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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927D LEU* 6.2 0.6 - - + +
930D LEU* 3.7 33.2 - - + +
931D LEU* 3.3 15.1 - - + +
934D SER* 3.5 28.4 - - - +
952D PRO 4.3 8.2 + - - +
954D LEU 5.1 0.8 + - - -
961D THR* 1.3 74.6 - - - +
963D LEU* 1.3 57.5 + - - +
965D ASN* 3.3 2.1 + - - +
966D ALA* 3.0 25.3 + - - +
978D LEU* 3.7 10.1 - - + -
983D VAL* 6.4 0.2 - - + -
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Residues in contact with LEU 963 (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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961D THR* 3.2 9.7 + - - +
962D ALA* 1.3 75.1 - - - +
964D HIS* 1.3 65.5 + - - +
966D ALA* 3.4 0.6 + - - -
967D VAL* 3.0 37.2 + - + +
975D VAL* 4.0 18.4 - - + +
978D LEU* 3.7 12.4 - - + +
979D VAL* 3.9 28.9 - - + -
983D VAL* 4.0 20.8 - - + +
984D ASN 4.0 3.4 - - - +
985D VAL* 3.8 25.1 - - + -
995D PRO* 3.7 28.7 - - + -
1011D LEU* 4.8 1.1 - - + -
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Residues in contact with HIS 964 (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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959D GLY 3.8 15.3 - - - -
960D ILE* 3.8 22.0 - - + -
961D THR* 2.7 43.4 + - + +
963D LEU* 1.3 79.7 - - - +
965D ASN* 1.3 62.5 + - - +
967D VAL* 3.8 4.0 - - - +
968D CYS* 2.9 32.7 + - - -
987D ALA* 3.0 29.2 + - + -
989D ASP* 4.4 1.2 + - + -
993D TRP* 3.0 27.1 + - + -
995D PRO* 3.7 16.1 - - + +
998D CYS* 3.8 24.2 - - - -
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Residues in contact with ASN 965 (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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407A GOL 5.7 0.8 + - - -
931D LEU* 3.0 45.4 + - - +
934D SER 4.0 2.0 - - - -
935D LEU* 3.6 38.3 - - + +
956D ASN* 5.9 0.8 - - - +
960D ILE* 3.2 21.5 - - - +
961D THR 3.2 5.6 + - - -
962D ALA 3.3 7.1 + - - +
964D HIS* 1.3 78.9 - - - +
966D ALA* 1.3 64.2 + - - +
968D CYS* 3.9 4.9 - - - +
969D ALA* 3.0 27.7 + - - +
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Residues in contact with ALA 966 (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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934D SER* 3.5 13.3 + - - +
962D ALA 3.0 17.5 + - - +
963D LEU* 3.8 3.8 - - - +
964D HIS 3.3 0.2 - - - -
965D ASN* 1.3 76.0 - - - +
967D VAL* 1.3 62.1 + - - +
969D ALA 3.9 0.2 - - - -
970D GLY* 3.2 3.1 + - - -
971D HIS* 3.1 27.7 + - - -
974D ILE* 3.9 29.2 - - + -
975D VAL* 3.5 21.5 - - + +
978D LEU* 4.3 5.2 - - + -
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Residues in contact with VAL 967 (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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963D LEU* 3.0 32.2 + - + +
964D HIS* 3.8 3.6 - - - +
966D ALA* 1.3 74.2 - - - +
968D CYS* 1.3 66.1 + - - +
970D GLY* 3.1 13.5 + - - -
975D VAL* 3.8 24.5 - - + -
995D PRO* 3.6 18.8 - - + +
998D CYS* 3.8 5.8 - - + -
999D ALA* 3.4 40.6 - - + +
1002D CYS* 4.5 6.1 - - - +
1004D ASN* 5.1 5.9 + - - +
1007D VAL* 4.2 12.1 - - + +
1011D LEU* 4.4 2.5 - - + -
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Residues in contact with CYS 968 (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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935D LEU* 5.8 3.4 - - + -
960D ILE* 6.6 0.4 - - - -
964D HIS* 2.9 23.9 + - - +
965D ASN* 4.0 5.6 - - - +
967D VAL* 1.3 77.5 - - - +
969D ALA* 1.3 59.8 + - - +
970D GLY 3.5 0.3 + - - -
998D CYS* 3.6 32.3 - - - -
1001D SER* 6.0 0.4 - - - -
1002D CYS* 4.0 21.6 - - - -
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Residues in contact with ALA 969 (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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935D LEU* 3.3 35.2 - - + +
965D ASN 3.0 16.8 + - - +
968D CYS* 1.3 76.7 - - - +
970D GLY* 1.3 61.9 + - - +
971D HIS* 3.4 23.3 + - + +
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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