Contacts of the helix formed by residues 833 - 841 (chain A) in PDB entry 1L8A
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 833 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ASN* 3.8 6.1 - - - +
832A ASP* 1.3 86.1 + - - +
834A ARG* 1.3 65.4 + - - +
835A GLU* 3.6 8.1 + - - +
836A ASN* 3.0 31.2 + - - +
837A LEU* 3.0 22.2 + - - +
101B LEU* 4.2 35.4 - - - -
103B LEU* 3.7 6.5 - - - +
167B GLN* 4.2 1.3 + - - -
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Residues in contact with ARG 834 (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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631A THR 3.6 14.6 - - - +
632A THR* 2.9 21.3 + - - +
634A ASN* 3.3 23.5 + - - +
693A ASN* 3.0 45.9 + - - +
694A GLU* 3.5 37.8 - - - +
695A ASN 5.5 0.2 - - - +
833A SER* 1.3 73.1 - - - +
835A GLU* 1.3 58.0 + - - +
837A LEU* 3.3 1.8 + - - +
838A ARG* 2.8 58.0 + - - +
101B LEU 4.9 1.7 + - - +
102B GLU* 3.9 24.8 - - - +
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Residues in contact with GLU 835 (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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833A SER* 3.2 8.4 - - - +
834A ARG* 1.3 79.5 - - - +
836A ASN* 1.3 69.2 + - - +
838A ARG* 3.4 7.0 + - - +
839A HIS* 3.2 23.2 + - + +
844A ASP* 4.8 1.6 - - - +
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Residues in contact with ASN 836 (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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832A ASP* 2.7 39.5 + - - +
833A SER* 3.0 15.4 + - - +
835A GLU* 1.3 85.3 - - - +
837A LEU* 1.3 58.4 + - - +
839A HIS* 3.4 5.0 + - - +
840A HIS* 2.9 30.1 + - - +
167B GLN* 3.7 10.3 + - - +
169B VAL* 4.2 7.9 - - + +
170B HIS* 3.7 28.8 + - - -
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Residues in contact with LEU 837 (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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631A THR* 3.6 24.0 - - + +
634A ASN* 3.5 27.6 - - + +
641A GLU* 3.4 30.5 - - - +
830A ARG* 3.6 22.2 - - + +
832A ASP* 3.7 7.4 - - + -
833A SER 3.0 17.5 + - - +
834A ARG 3.8 1.3 - - - +
836A ASN* 1.3 75.0 - - - +
838A ARG* 1.3 60.1 + - - +
840A HIS* 4.2 1.6 - - + -
841A PHE* 2.9 44.6 + - + +
169B VAL* 3.7 25.6 - - + -
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Residues in contact with ARG 838 (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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631A THR* 2.9 27.7 + - + +
632A THR* 3.1 24.5 + - - +
694A GLU* 2.9 42.2 + - - -
733A SER* 3.6 5.5 + - - -
734A ILE* 4.0 14.6 - - + +
736A ARG* 3.8 2.6 - - - +
737A HIS* 3.2 37.8 + - + -
834A ARG* 2.8 41.7 + - - +
835A GLU* 3.9 6.3 - - - +
837A LEU* 1.3 75.8 - - - +
839A HIS* 1.3 59.0 + - - +
841A PHE 4.2 0.4 - - - -
842A GLU 3.6 0.3 + - - -
843A VAL* 3.1 31.0 + - + -
844A ASP* 3.1 24.2 + - + -
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Residues in contact with HIS 839 (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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835A GLU* 3.2 16.0 + - + +
836A ASN* 3.8 6.5 - - - +
837A LEU 3.2 0.2 - - - -
838A ARG* 1.3 77.4 - - - +
840A HIS* 1.3 66.2 + - - +
842A GLU* 3.0 12.1 + - - +
844A ASP* 2.6 24.5 + - - +
846A SER* 3.4 20.0 - - - -
847A TYR* 3.3 33.6 + + - -
874A PHE 3.7 13.9 - - - -
875A ASN* 3.0 24.2 + - + +
876A ILE* 3.9 4.2 - - + +
877A ASP 5.9 0.9 - - - -
880A LYS* 4.2 4.8 + - - -
170B HIS* 6.3 2.7 - + - -
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Residues in contact with HIS 840 (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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830A ARG* 3.6 32.1 + - - -
836A ASN 2.9 19.0 + - - +
837A LEU* 3.7 4.5 - - - +
839A HIS* 1.3 77.3 - - - +
841A PHE* 1.3 79.5 + + - +
842A GLU 3.2 2.3 + - - -
880A LYS* 2.8 38.7 + - - +
881A VAL 5.8 0.4 + - - -
883A PRO* 3.2 30.3 - - + +
886A ALA* 3.8 19.2 - - + +
169B VAL* 4.0 35.6 - - + +
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Residues in contact with PHE 841 (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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630A ARG* 3.5 22.7 - - + -
631A THR* 3.8 14.4 - - + -
641A GLU* 4.4 4.7 - - - -
805A LYS* 5.9 0.5 - - - -
824A GLY 3.1 17.8 - - - +
825A THR* 3.5 35.4 - - + -
826A ASP 3.3 27.4 - - - -
827A GLY* 3.7 8.1 - - - -
828A PHE 3.3 23.6 - - - -
829A GLY* 3.9 8.7 - - - -
830A ARG* 5.0 0.4 - - + -
837A LEU* 2.9 38.1 + - + +
840A HIS* 1.3 91.1 - + - +
842A GLU* 1.3 72.0 + - - +
843A VAL* 3.4 4.0 + - + +
883A PRO* 4.0 13.9 - - + +
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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