Contacts of the helix formed by residues 914 - 925 (chain D) in PDB entry 7KHI
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 914 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1279C GLU 4.0 11.3 + - - +
1280C ALA 4.8 0.3 - - - +
1281C TYR 5.8 0.6 + - - -
805D GLN 5.2 0.7 - - - +
807D LEU 3.9 7.9 - - - +
808D VAL* 4.2 11.4 - - + -
912D GLY 3.5 2.0 + - - -
913D GLU* 1.3 71.9 - - - +
915D ILE* 1.3 63.6 + - - +
916D GLY 3.4 1.1 - - - -
917D VAL* 3.7 18.9 - - + +
918D ILE* 3.1 27.9 + - - +
1347D LEU* 4.3 8.1 - - + -
1359D ALA* 3.8 23.8 - - + +
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Residues in contact with ILE 915 (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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807D LEU* 3.3 30.5 + - + +
808D VAL* 4.5 1.3 - - - +
809D VAL* 4.3 20.6 - - + +
885D VAL* 6.0 0.2 - - + -
894D VAL* 4.6 8.7 - - + -
899D TYR* 3.0 54.1 - - + +
903D LEU* 5.1 3.6 - - + -
909D ILE* 5.6 4.7 - - + -
913D GLU* 3.1 10.3 + - + +
914D ALA* 1.3 71.9 - - - +
916D GLY* 1.3 67.5 + - - +
918D ILE* 3.3 18.3 + - + -
919D ALA* 2.9 23.2 + - + +
1252D HIS* 5.0 2.7 - - - +
1255D VAL* 4.4 10.8 - - + -
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Residues in contact with GLY 916 (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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804D ALA* 3.3 33.5 - - - +
807D LEU* 3.0 24.5 + - - -
915D ILE* 1.3 79.9 - - - +
917D VAL* 1.3 56.9 + - - +
919D ALA* 3.2 5.1 + - - +
920D ALA* 3.0 26.2 + - - +
1255D VAL* 5.1 1.6 - - - -
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Residues in contact with VAL 917 (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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1276C TRP* 4.2 29.4 - - + +
1279C GLU* 4.2 27.1 - - + +
1280C ALA* 4.3 2.7 - - - +
801D VAL* 4.6 15.0 - - + -
804D ALA 4.1 2.6 + - - -
805D GLN* 4.2 21.3 + - + +
914D ALA* 3.7 25.5 - - + +
916D GLY* 1.3 72.9 - - - +
918D ILE* 1.3 61.3 + - - +
920D ALA* 4.2 5.6 - - - -
921D GLN* 2.8 40.0 + - + +
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Residues in contact with ILE 918 (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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1280C ALA* 3.2 42.6 - - + +
431D ARG* 3.3 27.8 - - - +
493D PRO* 5.2 10.8 - - + +
899D TYR* 4.9 1.1 - - - +
903D LEU* 5.1 9.2 - - + -
913D GLU* 4.4 7.6 - - + +
914D ALA 3.1 17.7 + - - +
915D ILE* 3.3 24.4 + - + +
916D GLY 3.2 0.2 - - - -
917D VAL* 1.3 79.8 - - - +
919D ALA* 1.3 59.1 + - - +
921D GLN* 3.3 4.7 + - - +
922D SER* 2.9 27.4 + - - -
1252D HIS* 4.2 14.1 - - + -
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Residues in contact with ALA 919 (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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915D ILE* 2.9 14.9 + - + +
916D GLY 3.6 2.0 - - - +
918D ILE* 1.3 76.6 - - - +
920D ALA* 1.3 63.9 + - - +
922D SER* 3.2 1.4 + - - -
923D ILE* 2.9 29.8 + - - +
1252D HIS* 3.3 31.2 - - + +
1255D VAL* 3.2 36.1 - - + -
1256D ILE* 4.8 2.0 - - + -
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Residues in contact with ALA 920 (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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797D THR* 4.9 1.9 - - - +
800D LEU* 3.6 31.1 - - - +
801D VAL* 3.3 32.7 - - + +
804D ALA* 4.6 4.0 - - + -
916D GLY 3.0 16.7 + - - +
917D VAL* 3.8 5.4 - - - +
919D ALA* 1.3 75.9 - - - +
921D GLN* 1.3 57.6 + - - +
923D ILE* 3.3 2.0 + - - +
924D GLY* 2.9 26.7 + - - -
1256D ILE* 4.7 3.9 - - + +
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Residues in contact with GLN 921 (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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1273C MET 4.4 2.2 + - - -
1276C TRP* 3.4 23.3 - - + +
1277C ALA* 3.3 31.9 - - - +
1280C ALA* 3.9 5.6 - - - +
428D THR 5.4 1.4 + - - -
429D LEU 4.4 8.9 + - - +
430D HIS* 3.9 12.0 - - + +
431D ARG* 2.6 38.6 + - - +
797D THR* 5.6 4.5 - - + -
801D VAL* 5.1 6.1 - - + -
917D VAL* 2.8 25.7 + - + +
918D ILE* 3.7 4.9 - - + +
920D ALA* 1.3 76.6 - - - +
922D SER* 1.3 59.6 + - - +
924D GLY* 4.4 0.9 - - - +
925D GLU* 2.9 35.3 + - - +
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Residues in contact with SER 922 (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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430D HIS* 5.8 0.9 - - - -
493D PRO* 4.8 9.2 - - - -
494D ALA* 3.1 36.3 - - - +
918D ILE 2.9 17.2 + - - -
919D ALA 3.2 4.5 + - - -
921D GLN* 1.3 76.1 - - - +
923D ILE* 1.3 60.1 + - - +
925D GLU* 3.9 7.6 - - - +
926D PRO* 2.9 25.5 - - - +
1248D ILE* 4.6 4.0 - - - +
1252D HIS* 3.6 25.4 - - - -
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Residues in contact with ILE 923 (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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796D LEU* 5.8 3.4 - - + +
800D LEU* 3.4 28.9 - - + +
919D ALA 2.9 20.5 + - - +
922D SER* 1.3 78.6 - - - +
924D GLY* 1.3 61.1 + - - +
926D PRO* 3.5 13.6 - - - +
1145D PHE* 4.2 14.4 - - + -
1241D TYR* 3.9 25.8 + - + +
1248D ILE* 3.5 37.0 - - + -
1252D HIS* 3.8 19.7 - - + +
1253D ILE* 3.9 19.5 - - + +
1256D ILE* 5.1 5.4 - - + -
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Residues in contact with GLY 924 (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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429D LEU* 5.1 3.4 - - - +
793D SER* 4.4 7.1 + - - -
796D LEU* 6.0 3.1 - - - -
797D THR* 3.0 34.8 + - - -
800D LEU* 4.7 2.7 - - - +
920D ALA 2.9 16.8 + - - -
921D GLN 3.7 0.4 - - - -
923D ILE* 1.3 75.4 - - - +
925D GLU* 1.3 58.1 + - - +
926D PRO 2.4 22.9 - - - +
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Residues in contact with GLU 925 (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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429D LEU* 4.2 27.9 + - + +
430D HIS* 3.7 46.7 + - + +
494D ALA* 4.4 13.8 - - + +
797D THR* 5.3 0.2 - - - +
921D GLN 2.9 21.7 + - - +
922D SER* 3.9 7.8 - - - +
924D GLY* 1.3 71.7 - - - +
926D PRO* 1.4 91.5 - - + +
928D THR* 3.9 12.6 + - - -
929D GLN* 5.9 0.5 + - - -
68M ASN* 5.2 7.8 + - - -
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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