Contacts of the helix formed by residues 708 - 722 (chain A) in PDB entry 5MQF
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 708 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693A ILE* 6.1 4.3 - - - -
704A ASN 3.7 10.8 + - - -
705A LYS* 3.4 14.3 + - - -
706A ALA 3.2 1.0 - - - -
707A ARG* 1.3 76.3 - - - +
709A ILE* 1.3 58.9 + - - +
710A LEU 3.2 0.2 - - - -
711A GLN* 4.1 6.7 - - - +
712A HIS* 2.9 34.5 + - - +
247C ILE* 4.9 9.8 - - - +
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Residues in contact with ILE 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ARG* 6.1 4.7 - - + +
690A MET* 6.3 3.4 - - + -
705A LYS 3.9 4.2 + - - +
706A ALA* 3.3 14.0 + - - +
707A ARG 3.2 1.0 - - - -
708A THR* 1.3 79.1 - - - +
710A LEU* 1.3 50.1 + - - +
712A HIS* 4.9 2.0 - - - -
713A LEU* 2.6 42.0 + - + +
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Residues in contact with LEU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182 U 4.9 14.6 - - + +
192 G 6.2 0.9 - - - -
202 G 3.8 22.7 - - - +
706A ALA 4.3 1.0 + - - +
707A ARG* 3.2 13.2 + - + +
708A THR 3.2 0.8 - - - -
709A ILE* 1.3 77.9 - - - +
711A GLN* 1.3 61.2 + - - +
713A LEU* 4.3 1.3 - - - -
714A SER* 2.9 34.7 + - - -
250C CYS* 5.2 5.5 - - + +
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Residues in contact with GLN 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A ARG 3.5 7.8 + - - +
708A THR* 3.4 8.8 + - - +
710A LEU* 1.3 77.8 - - - +
712A HIS* 1.3 51.7 + - - +
714A SER* 5.3 0.4 - - - -
715A GLU* 2.6 41.9 + - - +
248C PRO* 4.9 10.8 - - + +
249C PRO 4.5 8.3 - - - +
250C CYS* 4.1 25.0 - - + +
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Residues in contact with HIS 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A THR* 2.9 18.2 + - - +
709A ILE* 4.6 2.5 - - - +
711A GLN* 1.3 74.7 - - - +
713A LEU* 1.3 60.9 + - - +
715A GLU* 3.9 4.2 - - - +
716A ALA* 2.9 31.9 + - - +
739A ILE* 4.1 25.8 - - + +
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Residues in contact with LEU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202 G 5.7 2.9 - - - +
212 C 5.0 9.4 - - - +
686A ARG* 6.4 1.6 - - + -
709A ILE* 2.6 24.9 + - - +
710A LEU* 3.9 3.6 - - - +
711A GLN 3.4 0.2 - - - -
712A HIS* 1.3 78.9 - - - +
714A SER* 1.3 58.1 + - - +
716A ALA* 3.1 4.1 + - - +
717A TRP* 2.9 26.8 + - - +
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Residues in contact with SER 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212 C 5.2 6.0 + - - -
710A LEU 2.9 18.8 + - - -
711A GLN* 4.8 0.9 - - - -
713A LEU* 1.3 74.4 - - - +
715A GLU* 1.3 58.4 + - - +
717A TRP* 3.4 9.4 - - - +
718A ARG* 2.9 32.4 + - - +
253C ASN* 4.8 16.1 - - - +
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Residues in contact with GLU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711A GLN 2.6 25.4 + - - +
712A HIS* 3.9 5.4 - - - +
714A SER* 1.3 76.6 - - - +
716A ALA* 1.3 49.6 + - - +
718A ARG* 5.3 1.8 - - - -
719A CYS* 2.5 39.3 + - - +
726A TRP* 3.5 21.0 - - + +
253C ASN* 6.0 1.6 - - - -
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Residues in contact with ALA 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A HIS 2.9 18.6 + - - +
713A LEU* 3.5 4.9 - - - +
715A GLU* 1.3 77.8 - - - +
717A TRP* 1.3 58.9 + - - +
719A CYS* 3.7 5.4 - - - -
720A TRP* 2.9 33.1 + - - +
739A ILE* 4.9 2.0 - - + +
743A VAL* 3.7 29.6 - - + -
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Residues in contact with TRP 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212 C 5.1 8.5 - - - +
222 U 5.3 9.2 - - - +
713A LEU 2.9 13.2 + - - +
714A SER* 3.1 13.7 + - - +
716A ALA* 1.3 75.9 - - - +
718A ARG* 1.3 58.9 + - - +
720A TRP* 4.6 0.2 - - - +
721A LYS* 2.9 36.4 + - - +
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Residues in contact with ARG 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A SER 2.9 16.4 + - - +
715A GLU* 4.7 2.0 - - - +
717A TRP* 1.3 74.6 - - - +
719A CYS* 1.3 56.4 + - - +
721A LYS* 4.5 3.6 - - - -
722A ALA* 2.9 38.7 + - + +
724A ILE* 4.5 3.9 - - + +
726A TRP* 5.3 2.2 - - + -
253C ASN* 4.3 26.0 - - + -
254C TRP* 5.6 1.3 - - + +
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Residues in contact with CYS 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A GLU 2.5 26.5 + - - +
716A ALA* 3.5 7.9 - - - +
717A TRP 3.2 0.4 - - - -
718A ARG* 1.3 76.8 - - - +
720A TRP* 1.3 58.7 + - - +
722A ALA 2.8 23.9 - - - +
724A ILE 3.6 16.7 - - - +
725A PRO 4.5 4.3 - - - +
726A TRP* 3.7 15.8 - - + +
743A VAL* 6.4 0.2 - - + -
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Residues in contact with TRP 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A ALA 2.9 17.4 + - - +
719A CYS* 1.3 76.4 - - + +
721A LYS* 1.3 61.7 + - - +
722A ALA 3.4 4.7 + - - +
743A VAL* 5.1 8.3 - - + +
747A ALA* 4.4 23.1 - - + -
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Residues in contact with LYS 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 U 6.0 2.2 - - - +
252 G 5.8 3.8 - - - +
717A TRP* 2.9 22.6 + - - +
718A ARG* 4.5 2.7 - - - +
720A TRP* 1.3 77.3 - - - +
722A ALA* 1.3 58.8 + - + +
781A ARG* 5.8 4.7 - - - +
1022A MET* 5.5 3.6 - - - +
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Residues in contact with ALA 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A ARG* 2.9 23.7 + - + +
719A CYS 2.8 15.1 - - - +
720A TRP 3.6 5.4 - - - +
721A LYS* 1.3 78.1 - - + +
723A ASN* 1.3 61.7 + - - +
724A ILE* 3.4 11.4 - - + +
1022A MET* 5.4 11.4 - - + -
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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