Contacts of the helix formed by residues 994 - 1002 (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 994 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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964D HIS* 3.8 2.9 - - - -
985D VAL 5.0 0.4 - - - -
986D ASN* 3.8 28.0 + - + +
987D ALA 3.4 2.5 - - - +
988D ALA* 4.4 5.4 - - + -
992D GLY 3.8 9.2 - - - +
993D TRP* 1.3 75.6 - - - +
995D PRO* 1.3 75.8 - - - +
996D LEU* 3.3 11.3 + - - +
997D HIS* 2.9 47.8 + - + +
998D CYS* 3.0 12.3 + - - -
1017D ALA 5.3 0.5 + - - -
1020D ALA* 4.1 17.9 - - + +
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Residues in contact with PRO 995 (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* 5.3 0.4 - - - +
963D LEU* 3.7 33.4 - - + +
964D HIS* 3.7 16.1 - - + +
967D VAL* 3.6 12.5 - - + +
984D ASN 4.6 1.6 - - - +
985D VAL 3.3 28.3 - - - +
987D ALA* 3.3 17.7 - - + +
994D THR* 1.3 83.6 - - - +
996D LEU* 1.3 56.4 + - - +
998D CYS* 3.1 9.7 + - + +
999D ALA* 2.8 26.2 + - - +
1011D LEU* 3.7 15.5 - - + -
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Residues in contact with LEU 996 (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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985D VAL 5.0 0.8 + - - -
986D ASN* 5.8 0.9 - - - +
994D THR* 3.1 10.5 + - - +
995D PRO* 1.3 74.4 - - - +
997D HIS* 1.3 60.9 + - - +
999D ALA* 3.3 0.7 + - - +
1000D ALA* 2.9 32.2 + - - +
1008D CYS* 3.8 37.9 - - + +
1011D LEU* 3.7 19.8 - - + +
1012D VAL* 4.2 7.6 - - + -
1016D ALA* 4.1 23.8 - - + -
1017D ALA 4.1 16.8 - - - +
1018D VAL* 4.1 13.9 - - + +
1029D ALA* 3.6 21.5 - - + -
1047D LEU* 4.4 11.9 - - + -
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Residues in contact with HIS 997 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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992D GLY 3.7 14.3 + - - -
993D TRP* 3.5 21.9 - - + -
994D THR* 2.9 44.6 + - + +
996D LEU* 1.3 75.3 - - - +
998D CYS* 1.3 57.4 + - - +
1000D ALA* 3.5 1.9 + - - +
1001D SER* 3.0 28.8 + - - -
1020D ALA* 3.1 36.9 + - + -
1021D MET 4.2 0.9 - - - -
1022D THR* 3.7 18.0 - - + +
1027D GLN 3.2 12.5 + - - -
1028D THR 3.5 6.3 - - - -
1029D ALA* 3.4 25.3 + - + +
1032D LYS* 3.9 8.0 - - + +
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Residues in contact with CYS 998 (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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960D ILE* 6.1 1.8 - - - -
964D HIS* 3.8 23.3 - - - -
967D VAL* 3.8 10.5 - - + -
968D CYS* 3.6 32.1 - - - -
993D TRP* 4.2 17.9 - - - -
994D THR 3.0 16.4 + - - -
995D PRO* 3.1 8.0 + - + +
997D HIS* 1.3 74.3 - - - +
999D ALA* 1.3 66.1 + - - +
1001D SER* 2.8 23.4 + - - -
1002D CYS* 3.2 13.1 + - - -
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Residues in contact with ALA 999 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967D VAL* 3.4 16.9 - - + +
995D PRO 2.8 20.0 + - - +
996D LEU 3.8 2.5 - - - +
998D CYS* 1.3 72.0 - - - +
1000D ALA* 1.3 63.1 + - - +
1002D CYS* 3.1 11.9 + - - +
1004D ASN* 3.1 27.1 + - - +
1007D VAL* 3.8 21.5 - - + -
1008D CYS* 3.6 19.7 - - - +
1011D LEU* 4.1 5.8 - - + -
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Residues in contact with ALA1000 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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996D LEU 2.9 17.3 + - - +
997D HIS 3.7 3.8 - - - +
999D ALA* 1.3 77.2 - - - +
1001D SER* 1.3 57.2 + - - +
1003D ASN* 2.8 19.2 + - - +
1008D CYS* 3.6 9.3 - - - -
1029D ALA 3.0 29.4 - - - +
1032D LYS* 4.2 0.7 - - + -
1033D CYS* 3.4 21.4 - - - -
1043D CYS* 4.2 4.0 - - - -
1047D LEU* 3.6 18.6 - - + -
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Residues in contact with SER1001 (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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968D CYS* 6.0 0.5 - - - -
993D TRP* 3.8 21.5 - - - -
997D HIS 3.0 15.2 + - - -
998D CYS* 2.8 19.2 + - - -
1000D ALA* 1.3 75.2 - - - +
1002D CYS* 1.3 62.4 + - - +
1003D ASN* 3.3 1.0 + - - -
1032D LYS* 3.3 19.9 + - - -
1034D GLU* 3.3 28.6 - - - +
1037D GLU* 5.8 0.2 - - - +
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Residues in contact with CYS1002 (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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967D VAL 4.5 4.7 - - - +
968D CYS* 4.0 32.1 - - - -
998D CYS* 3.2 17.2 + - - -
999D ALA* 3.1 9.6 + - - +
1000D ALA 3.1 1.2 - - - -
1001D SER* 1.3 79.7 - - - +
1003D ASN* 1.3 69.8 + - - +
1004D ASN* 3.1 12.7 + - + +
1037D GLU* 6.4 0.4 - - - -
1038D GLU 4.8 0.2 - - - +
1202D EDO 3.3 15.6 - - - +
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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