Contacts of the helix formed by residues 707 - 722 (chain A) in PDB entry 5E2Q
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 ASP 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ARG* 4.4 1.0 + - - -
43A TYR* 2.7 38.3 + - - -
257A LYS* 2.4 28.6 + - - +
704A PHE* 3.8 4.9 + - - +
706A GLU* 1.3 81.8 + - - +
708A GLY* 1.3 64.7 + - - +
709A PRO* 3.5 3.6 - - - -
710A GLU* 3.1 29.2 + - + +
711A LEU* 3.1 24.3 + - - +
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Residues in contact with GLY 708 (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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64A SER* 5.0 0.2 + - - -
68A ARG* 3.3 16.4 - - - -
704A PHE* 3.0 30.9 + - - -
705A PRO 4.7 0.2 - - - -
706A GLU 3.8 0.6 - - - -
707A ASP* 1.3 73.7 - - - +
709A PRO* 1.3 71.6 - - - +
711A LEU* 3.0 16.9 + - - +
712A GLU* 3.2 13.9 + - - +
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Residues in contact with PRO 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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65A ARG* 5.6 3.6 + - - +
68A ARG* 3.8 30.0 - - - +
704A PHE 5.1 0.2 - - - +
705A PRO 5.8 1.3 - - - +
706A GLU 5.5 1.1 - - - +
707A ASP* 3.8 2.5 - - - -
708A GLY* 1.3 89.3 - - - +
710A GLU* 1.3 59.5 + - - +
711A LEU 3.4 0.2 - - - -
712A GLU* 3.6 19.7 + - - +
713A GLU* 3.3 20.4 + - - +
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Residues in contact with GLU 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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257A LYS* 3.2 35.1 + - - +
707A ASP* 3.1 20.5 + - + +
708A GLY 3.1 1.0 - - - -
709A PRO* 1.3 77.6 - - - +
711A LEU* 1.3 61.2 + - - +
713A GLU* 3.2 8.5 + - + +
714A ILE* 2.9 45.5 + - + +
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Residues in contact with LEU 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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43A TYR* 3.8 24.7 - - + -
46A LEU* 3.7 25.8 - - + -
60A TYR* 5.4 3.8 - - + -
254A ILE* 5.9 5.6 - - + -
257A LYS* 4.4 21.8 - - + -
704A PHE* 3.5 46.0 - - + -
707A ASP* 3.1 11.6 + - - +
708A GLY 3.0 6.0 + - - +
710A GLU* 1.3 74.5 - - - +
712A GLU* 1.3 59.7 + - + +
714A ILE* 3.6 12.6 - - + +
715A LEU* 2.9 38.6 + - + +
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Residues in contact with GLU 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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60A TYR* 5.1 4.7 - - + -
61A ALA* 4.0 20.4 - - + +
64A SER* 2.4 29.5 + - - +
65A ARG* 3.2 37.6 + - - +
68A ARG* 2.3 35.8 + - - -
708A GLY 3.5 7.6 - - - +
709A PRO* 3.6 19.4 - - - +
710A GLU 3.3 0.2 - - - -
711A LEU* 1.3 75.6 - - - +
713A GLU* 1.3 56.6 + - - +
715A LEU* 3.7 4.8 + - - +
716A THR* 2.6 35.5 + - - -
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Residues in contact with GLU 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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65A ARG* 4.5 14.5 + - - +
139A GLU* 5.6 1.0 - - - +
709A PRO 3.3 10.2 + - - +
710A GLU* 3.2 12.2 + - + +
712A GLU* 1.3 78.1 - - - +
714A ILE* 1.3 60.7 + - + +
716A THR* 3.3 10.1 + - - +
717A GLN* 2.9 31.1 + - + +
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Residues in contact with ILE 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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253A PRO* 3.7 44.4 - - + +
254A ILE* 3.9 13.9 - - + -
257A LYS* 4.6 4.5 - - + -
710A GLU* 2.9 40.1 + - + +
711A LEU* 3.6 20.4 - - + +
713A GLU* 1.3 77.8 - - + +
715A LEU* 1.3 63.2 + - + +
717A GLN* 3.1 8.1 + - - +
718A LEU* 3.0 40.0 + - + +
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Residues in contact with LEU 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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46A LEU* 3.6 37.7 - - + +
49A LEU* 3.8 12.6 - - + -
50A LEU* 4.4 11.6 - - + +
57A PRO* 3.6 21.2 - - + +
60A TYR* 3.5 38.1 - - + -
61A ALA* 5.5 0.2 - - + -
254A ILE* 3.7 24.0 - - + -
711A LEU* 2.9 21.4 + - - +
712A GLU* 4.1 4.3 - - - +
714A ILE* 1.3 77.1 - - + +
716A THR* 1.3 61.4 + - - +
718A LEU* 3.7 5.3 + - - +
719A ALA* 3.2 23.6 + - - +
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Residues in contact with THR 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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57A PRO* 5.4 0.9 - - - -
58A TYR* 4.2 20.5 - - + -
61A ALA* 3.7 16.3 - - - +
143A LEU* 4.2 12.3 - - + +
712A GLU 2.6 23.9 + - - -
713A GLU* 3.5 11.4 - - - +
715A LEU* 1.3 76.3 - - - +
717A GLN* 1.3 62.8 + - - +
719A ALA* 3.3 5.8 + - - +
720A THR* 3.1 30.1 + - + +
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Residues in contact with GLN 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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253A PRO* 4.4 11.6 - - - +
713A GLU* 2.9 18.3 + - + +
714A ILE* 3.1 10.3 + - - +
716A THR* 1.3 76.7 - - - +
718A LEU* 1.3 85.5 + - - +
720A THR* 2.9 22.9 + - - +
721A ALA* 3.1 20.6 + - - +
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Residues in contact with LEU 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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50A LEU* 3.7 36.2 - - + +
249A GLY 5.6 2.0 - - - +
250A ASP* 6.0 0.4 - - - +
251A TYR* 4.2 18.4 - - - +
252A ALA 4.8 0.4 - - - +
253A PRO* 4.0 16.2 - - + -
254A ILE* 3.8 20.9 - - + -
714A ILE* 3.0 30.7 + - + +
715A LEU* 4.1 2.2 - - - +
717A GLN* 1.3 93.4 - - - +
719A ALA* 1.3 63.9 + - - +
721A ALA* 3.6 11.4 + - + +
722A ASP* 3.6 21.3 + - - +
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Residues in contact with ALA 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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50A LEU* 4.1 6.7 - - - +
54A PRO 4.7 2.4 - - - +
57A PRO* 3.8 19.5 - - + -
58A TYR* 3.4 33.0 + - + -
715A LEU 3.2 19.3 + - - +
716A THR 3.5 3.1 - - - +
717A GLN 3.2 0.2 - - - -
718A LEU* 1.3 74.1 - - - +
720A THR* 1.3 64.7 + - - +
722A ASP* 3.2 14.4 + - - +
723A ALA* 3.3 10.7 + - - +
726A TRP* 5.2 3.6 - - - -
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Residues in contact with THR 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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58A TYR* 3.2 25.6 - - + +
716A THR* 3.1 20.0 + - + +
717A GLN* 2.9 20.7 + - - +
719A ALA* 1.3 75.5 - - - +
721A ALA* 1.3 62.4 + - - +
722A ASP 3.3 0.7 + - - -
723A ALA* 3.3 18.0 + - - +
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Residues in contact with ALA 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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717A GLN* 3.1 22.5 + - - +
718A LEU* 3.7 10.5 - - + +
719A ALA 3.2 0.2 - - - -
720A THR* 1.3 82.0 + - - +
722A ASP* 1.3 67.7 + - - +
724A ARG* 3.5 18.4 + - - +
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Residues in contact with ASP 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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50A LEU* 5.5 2.4 - - - +
199A ARG* 3.5 17.2 + - - -
215A ARG* 3.2 36.7 + - - -
250A ASP* 4.7 0.3 - - - +
718A LEU* 3.6 15.0 + - - +
719A ALA* 3.2 6.0 + - - +
720A THR 3.2 0.2 - - - -
721A ALA* 1.3 85.6 - - - +
723A ALA* 1.3 63.7 + - - +
724A ARG* 3.2 4.8 + - - +
725A PHE* 3.1 34.6 + - + +
726A TRP* 3.2 28.3 - - + -
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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