Contacts of the helix formed by residues 707 - 720 (chain A) in PDB entry 1U1H
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 SER 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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705A ILE 5.0 1.1 - - - -
706A PRO* 1.3 75.0 - - - +
708A SER* 1.3 66.1 + - - +
709A GLU* 2.7 37.4 + - - +
710A GLU* 2.9 23.8 + - - +
711A ILE* 2.9 23.5 + - - +
749A ASN* 3.9 7.0 - - - +
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Residues in contact with SER 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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707A SER* 1.3 72.6 - - - +
709A GLU* 1.3 56.6 + - - +
711A ILE* 4.5 1.3 - - - -
712A ALA* 2.9 33.8 + - - +
749A ASN* 3.1 49.7 + - - +
752A ASP* 3.8 19.3 + - - +
753A ALA* 3.7 3.9 - - - +
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Residues in contact with GLU 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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707A SER* 2.7 30.6 + - - +
708A SER* 1.3 78.8 - - - +
710A GLU* 1.3 72.6 + - + +
712A ALA* 3.9 3.4 - - - +
713A ASP* 3.0 27.7 + - - +
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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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705A ILE 4.9 1.6 - - - +
706A PRO* 4.3 9.9 - - + +
707A SER* 2.9 36.0 + - - +
709A GLU* 1.3 90.8 - - + +
711A ILE* 1.3 61.1 + - + +
713A ASP* 2.9 9.1 + - - +
714A ARG* 2.8 38.6 + - + +
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Residues in contact with ILE 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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697A VAL* 3.7 36.3 - - + +
698A TYR* 5.2 2.7 - - + -
706A PRO* 3.7 30.5 - - + -
707A SER 2.9 17.0 + - - +
708A SER* 4.2 0.4 - - - +
710A GLU* 1.3 72.4 - - - +
712A ALA* 1.3 64.6 + - - +
714A ARG* 3.0 11.9 + - - +
715A VAL* 3.0 26.5 + - + +
729A VAL* 5.0 0.4 - - + -
746A ALA 4.1 1.8 - - - +
749A ASN* 3.9 10.1 - - + -
750A MSE 3.5 41.3 - - + +
753A ALA* 3.6 18.6 - - + -
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Residues in contact with ALA 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 SER 2.9 22.2 + - - +
709A GLU* 3.9 4.5 - - - +
711A ILE* 1.3 76.6 - - - +
713A ASP* 1.3 63.0 + - - +
715A VAL* 3.2 7.7 + - - +
716A ASN* 3.1 29.5 + - - +
753A ALA* 3.3 24.8 - - + +
756A LEU* 4.7 11.0 - - + -
757A ILE* 3.9 14.8 - - + +
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Residues in contact with ASP 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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709A GLU 3.0 16.2 + - - +
710A GLU* 2.9 15.8 + - - +
712A ALA* 1.3 77.0 - - - +
714A ARG* 1.3 60.3 + - + +
716A ASN* 3.2 10.1 + - - +
717A LYS* 2.7 56.5 + - - +
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Residues in contact with ARG 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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672A ASN* 3.9 8.1 + - - -
673A SER* 3.6 36.3 + - - +
675A SER 3.0 22.8 + - - -
677A GLU* 2.6 36.4 + - - +
696A GLY 4.2 13.5 + - - -
697A VAL* 4.3 23.5 - - + +
710A GLU* 2.8 25.2 + - + +
711A ILE* 3.0 7.8 + - - +
713A ASP* 1.3 76.8 - - + +
715A VAL* 1.3 56.8 + - - +
717A LYS* 3.5 5.4 + - - +
718A MSE 2.9 37.8 + - - +
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Residues in contact with VAL 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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432A LEU* 4.0 26.7 - - + -
697A VAL* 4.3 9.4 - - + -
711A ILE* 3.0 25.3 + - + +
712A ALA* 3.6 10.1 - - - +
713A ASP 3.2 0.2 - - - -
714A ARG* 1.3 72.9 - - - +
716A ASN* 1.3 61.2 + - - +
718A MSE 3.4 20.6 - - + +
719A LEU* 2.9 33.5 + - + +
727A LEU* 4.2 11.2 - - + +
729A VAL* 4.3 19.5 - - + -
753A ALA* 5.4 2.5 - - + -
754A ALA* 5.8 2.0 - - - +
757A ILE* 4.4 9.6 - - + -
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Residues in contact with ASN 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 ALA* 3.1 17.2 + - - +
713A ASP* 3.2 10.7 + - - +
715A VAL* 1.3 74.0 - - - +
717A LYS* 1.3 68.1 + - + +
718A MSE 3.0 1.6 - - - -
719A LEU* 2.9 20.2 + - - +
720A ALA* 3.0 12.0 + - - +
757A ILE* 3.1 43.7 - - - +
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Residues in contact with LYS 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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677A GLU* 2.9 45.9 - - + +
678A LYS* 5.9 2.9 - - - +
713A ASP* 2.7 48.9 + - - +
714A ARG* 3.9 1.1 - - - +
716A ASN* 1.3 78.4 - - + +
718A MSE 1.3 59.4 + - - +
720A ALA* 3.0 26.0 - - - +
721A VAL* 4.0 5.4 + - - +
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Residues in contact with MSE 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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672A ASN* 5.2 1.1 - - - +
677A GLU* 4.3 9.0 - - + -
680A LEU* 3.5 22.0 - - + -
695A PRO* 3.6 33.4 - - - +
696A GLY 4.7 0.7 - - - +
697A VAL* 3.7 27.8 - - + -
714A ARG* 2.9 26.2 + - - +
715A VAL* 3.4 24.7 - - + +
717A LYS* 1.3 73.7 - - - +
719A LEU* 1.3 57.0 + - - +
720A ALA 3.0 4.5 - - - -
721A VAL* 2.8 31.4 + - - +
722A LEU* 3.0 7.4 + - + +
727A LEU* 4.0 31.6 - - + -
728A TRP 4.6 5.2 - - - +
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Residues in contact with LEU 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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432A LEU* 4.3 6.1 - - + -
715A VAL* 2.9 27.8 + - + +
716A ASN* 2.9 14.1 + - - +
718A MSE 1.3 75.4 - - - +
720A ALA* 1.3 62.0 + - - +
721A VAL 2.9 2.2 + - - -
722A LEU 3.0 20.6 + - - +
724A GLN* 3.3 38.6 - - + +
727A LEU* 3.4 24.0 - - + -
757A ILE* 3.7 30.3 - - + -
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Residues in contact with ALA 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 ASN 3.0 8.1 + - - +
717A LYS* 3.0 23.3 - - - +
718A MSE 3.0 0.4 - - - -
719A LEU* 1.3 76.6 - - - +
721A VAL* 1.3 61.7 + - + +
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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