Contacts of the helix formed by residues 707 - 720 (chain B) in PDB entry 6AHU
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 PRO 707 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701B LEU* 4.8 19.5 - - + +
704B PHE 4.0 7.2 - - - +
705B CYS 3.7 1.3 - - - -
706B CYS* 1.3 89.2 - - - +
708B TRP* 1.3 50.3 + - + +
709B GLU* 3.1 6.1 - - + -
710B GLN* 2.9 10.6 + - + +
711B LEU* 2.6 40.5 + - + -
951B PRO* 6.1 3.6 - - + -
955B VAL* 5.0 12.9 - - + +
966B PHE* 3.6 38.4 - - + -
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Residues in contact with TRP 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B ASP 5.5 3.8 - - - -
664B PRO* 3.7 35.1 - - + +
669B GLY 5.7 1.8 - - - -
670B MET* 4.3 19.2 - - - +
673B ALA* 5.1 9.9 - - + -
705B CYS* 3.1 46.7 - - + -
706B CYS* 3.5 5.3 - - + +
707B PRO* 1.3 77.2 - - + +
709B GLU* 1.3 68.8 + - + +
710B GLN 3.2 0.4 - - - -
711B LEU* 3.7 15.5 - - + -
712B THR* 3.1 34.8 + - + +
803B LEU* 3.6 27.6 - - + +
856B LEU* 4.7 14.1 - - + -
966B PHE* 4.2 25.4 - + + -
968B THR* 5.6 9.4 - - + -
984B PHE* 5.8 6.5 - + + -
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Residues in contact with GLU 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670B MET* 3.5 28.5 - - + +
706B CYS* 5.5 8.7 - - + +
707B PRO 3.1 1.7 - - - -
708B TRP* 1.3 83.7 - - + +
710B GLN* 1.3 64.5 + - + +
712B THR* 4.7 1.0 + - - -
713B GLN* 3.2 29.9 + - - +
802B HIS* 5.0 7.1 - - - +
803B LEU* 3.4 30.8 - - - +
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Residues in contact with GLN 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B PRO* 2.9 7.3 + - + +
709B GLU* 1.3 86.6 - - + +
711B LEU* 1.3 57.3 + - - +
712B THR 3.5 1.8 - - - -
713B GLN* 3.8 17.2 - - + +
714B ASP* 3.1 27.0 + - - +
951B PRO* 3.4 38.8 - - - +
952B LEU* 3.4 33.0 - - + +
955B VAL* 4.1 10.1 - - + +
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Residues in contact with LEU 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B PRO* 2.6 28.5 + - + +
708B TRP* 3.7 10.7 - - + +
710B GLN* 1.3 70.4 - - - +
712B THR* 1.3 65.1 + - + +
714B ASP* 3.1 12.8 + - - +
715B TRP* 3.2 46.1 + - + +
856B LEU* 6.6 0.2 - - + -
955B VAL* 3.8 19.3 - - + -
963B LEU* 4.5 17.7 - - + -
964B LEU 4.2 15.9 - - - +
965B GLY* 6.1 0.2 - - - -
966B PHE* 4.1 28.9 - - + -
986B SER* 4.5 9.9 - - - +
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Residues in contact with THR 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B TRP* 3.1 24.8 + - + +
709B GLU 4.7 0.3 + - - -
711B LEU* 1.3 79.3 - - + +
713B GLN* 1.3 64.6 + - - +
714B ASP 3.2 0.4 + - - -
715B TRP* 3.9 3.9 + - - +
716B GLU* 3.4 21.5 + - - +
803B LEU* 5.1 7.6 - - + +
854B ARG* 3.4 36.3 - - + +
855B ALA 4.3 11.9 - - - +
856B LEU* 4.3 18.8 - - + -
986B SER* 4.0 20.4 - - - +
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Residues in contact with GLN 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B GLU* 3.2 23.2 + - - +
710B GLN* 3.6 18.7 + - - +
711B LEU 3.2 0.6 - - - -
712B THR* 1.3 76.9 + - - +
714B ASP* 1.3 59.8 + - - +
716B GLU* 3.0 28.3 - - - +
717B SER* 3.5 9.9 - - - -
802B HIS* 6.0 0.2 - - - +
854B ARG* 3.6 41.2 - - - +
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Residues in contact with ASP 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B GLN 3.1 17.3 + - - +
711B LEU 3.1 6.2 + - - +
713B GLN* 1.3 77.6 - - - +
715B TRP* 1.3 68.0 + - - +
716B GLU 3.2 1.8 - - - -
717B SER* 3.0 21.4 + - - -
718B ARG* 3.1 15.9 + - - +
955B VAL* 3.1 38.6 - - + +
956B THR* 3.3 29.3 - - - +
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Residues in contact with TRP 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711B LEU* 3.2 49.0 + - + +
712B THR* 3.9 4.9 + - - +
713B GLN 3.6 0.2 - - - -
714B ASP* 1.3 85.2 + - - +
716B GLU* 1.3 58.4 + - - +
718B ARG* 3.4 46.3 + - - +
719B VAL* 3.9 20.6 - - + +
877B VAL* 4.8 6.1 - - + -
955B VAL* 5.7 3.1 + - - +
962B THR* 3.7 14.4 - - + -
963B LEU* 3.3 26.3 + - - +
964B LEU* 3.6 22.9 + - + +
986B SER* 4.8 10.8 - - - -
988B THR* 3.3 34.1 + - - +
989B GLY* 4.2 20.9 - - - -
992B ASP* 4.8 7.0 - - + -
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Residues in contact with GLU 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B THR 3.4 15.9 + - - +
713B GLN* 3.0 27.0 - - - +
715B TRP* 1.3 75.7 - - - +
717B SER* 1.3 63.8 + - - +
718B ARG 3.3 0.9 - - - -
719B VAL* 4.1 2.5 - - - +
720B GLN* 3.2 44.1 + - + +
853B PRO* 6.4 1.3 - - + -
854B ARG* 4.3 27.8 + - + +
988B THR* 5.4 5.2 - - + -
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Residues in contact with SER 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B GLN 3.5 13.5 - - - -
714B ASP* 3.0 15.5 + - - -
716B GLU* 1.3 86.5 - - - +
718B ARG* 1.3 61.6 + - - +
719B VAL 3.5 0.2 - - - -
720B GLN* 5.5 0.4 - - - -
721B ALA* 3.3 25.5 - - - +
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Residues in contact with ARG 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714B ASP* 3.1 15.4 + - - +
715B TRP* 3.4 48.4 - - + +
716B GLU 3.3 0.8 - - - -
717B SER* 1.3 79.9 - - - +
719B VAL* 1.3 65.1 + - + +
721B ALA* 4.6 0.4 - - - +
722B TYR* 4.3 13.0 + - - +
956B THR 5.9 0.8 + - - -
957B LEU* 5.7 7.4 - - - +
962B THR* 3.9 18.8 + - - +
992B ASP* 4.1 18.5 + - - -
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Residues in contact with VAL 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B TRP* 3.9 17.5 + - + +
716B GLU* 3.7 3.0 + - - +
718B ARG* 1.3 85.4 - - + +
720B GLN* 1.3 80.1 + - + +
721B ALA 3.2 1.3 - - - -
722B TYR* 3.3 19.5 + - - +
846B LEU* 5.3 13.5 - - + -
849B LEU* 5.6 7.6 - - + -
988B THR* 4.7 17.7 - - + +
992B ASP* 5.7 7.0 - - + +
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Residues in contact with GLN 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716B GLU* 3.2 31.1 + - + +
719B VAL* 1.3 89.4 - - + +
721B ALA* 1.3 58.0 + - - +
722B TYR 3.3 3.4 + - - -
849B LEU* 5.5 11.5 + - - +
850B GLY* 5.5 6.5 - - - -
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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