Contacts of the helix formed by residues 834 - 848 (chain A) in PDB entry 1N35
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 GLN 834 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ILE* 4.3 13.6 - - + +
242A THR 2.9 21.0 + - - +
243A ALA 4.0 15.2 + - - -
244A GLY* 4.1 4.0 - - - +
363A ARG* 3.0 40.3 - - - +
366A ARG* 4.6 2.6 - - - +
833A LEU* 1.3 68.9 - - - +
835A TRP* 1.3 66.5 + - - +
836A GLN 3.1 2.8 + - - -
837A ARG* 3.1 17.0 + - + -
838A TRP* 2.9 21.1 + - - +
1080A GLY 4.1 1.0 + - - -
1084A LEU* 3.0 25.7 - - - +
1085A ASN* 3.6 14.3 - - - +
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Residues in contact with TRP 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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169A ASP* 4.2 4.6 + - - -
170A PRO* 3.7 20.9 - - + -
833A LEU 2.9 6.9 + - - -
834A GLN* 1.3 69.8 - - - +
836A GLN* 1.3 77.4 + - + +
838A TRP* 3.7 0.5 - - - +
839A ILE* 2.8 54.1 + - + +
886A TRP* 3.4 31.4 - + + -
888A PHE 3.9 11.2 - - - -
889A SER* 5.0 0.9 - - - -
890A TRP* 3.6 28.5 - - + -
1085A ASN* 3.1 29.0 + - - -
1086A SER* 3.0 24.9 + - - +
1087A ASP* 3.4 16.2 - - + +
1088A PRO* 3.4 20.6 - - + -
1234A THR* 3.4 39.9 - - + -
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Residues in contact with GLN 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 4.1 18.3 - - + +
168A TYR 2.8 25.2 + - - +
169A ASP* 3.3 27.7 + - - +
170A PRO* 3.8 7.7 - - - +
176A ASP* 5.7 0.4 - - - +
834A GLN* 3.3 1.0 - - - +
835A TRP* 1.3 93.5 + - + +
837A ARG* 1.3 67.6 + - + +
839A ILE 3.1 0.9 + - - -
840A ARG* 2.9 26.4 + - - +
886A TRP* 3.0 62.5 - - + +
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Residues in contact with ARG 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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162A GLU* 2.5 42.6 + - - +
165A GLY 4.6 2.4 + - - -
166A SER* 4.1 8.7 - - - +
167A LEU* 3.3 21.0 - - - +
176A ASP* 3.0 35.1 + - - +
178A ILE* 3.7 33.3 + - + +
180A ASP* 6.1 0.6 - - - +
241A GLN* 3.7 25.0 + - - +
242A THR* 4.0 11.8 - - + +
834A GLN* 3.1 15.3 + - + +
836A GLN* 1.3 76.6 - - + +
838A TRP* 1.3 56.9 + - - +
840A ARG* 3.3 23.5 + - - +
841A TYR* 3.0 30.3 + - - +
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Residues in contact with TRP 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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242A THR* 3.8 21.1 - - + +
800A ILE* 4.1 19.5 - - + -
824A VAL* 3.0 44.2 - - + -
825A PHE* 3.0 41.0 + + - -
828A GLY* 3.4 15.0 - - - -
833A LEU* 3.6 32.8 - - + -
834A GLN 2.9 17.1 + - - +
835A TRP 3.7 2.9 - - - +
837A ARG* 1.3 76.2 - - - +
839A ILE* 1.3 59.4 + - - +
841A TYR* 3.4 24.9 + + - +
842A SER* 2.9 39.4 + - - -
890A TRP* 3.7 22.4 - + + -
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Residues in contact with ILE 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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825A PHE* 4.2 14.1 - - + -
835A TRP* 2.8 48.4 + - + +
836A GLN 3.8 2.7 - - - +
838A TRP* 1.3 72.7 - - - +
840A ARG* 1.3 63.5 + - - +
842A SER* 3.2 7.6 + - - -
843A TRP* 3.0 40.0 + - + -
875A LEU* 4.9 1.8 - - + -
876A PRO* 3.6 37.7 - - + +
877A LEU 5.5 1.1 - - - +
878A VAL* 4.2 3.1 - - + -
886A TRP* 3.8 17.5 - - + -
888A PHE 4.4 4.7 - - - +
890A TRP* 4.2 17.9 - - + +
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Residues in contact with ARG 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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16A ILE* 3.0 43.9 - - + +
17A SER* 3.2 22.1 + - - +
161A ALA* 2.9 30.5 + - + +
162A GLU* 3.2 25.7 + - - +
164A GLY* 3.5 6.7 - - - -
165A GLY 3.0 19.8 + - - -
167A LEU* 3.0 33.1 - - + +
836A GLN 2.9 16.8 + - - +
837A ARG* 3.3 17.4 + - - +
839A ILE* 1.3 78.8 - - - +
841A TYR* 1.3 62.8 + - - +
843A TRP* 3.1 9.9 + - - +
844A ALA* 3.1 19.1 + - - +
886A TRP* 4.0 6.3 - - + -
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Residues in contact with TYR 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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154A PHE* 3.2 29.1 + - - -
157A ALA* 3.7 5.6 - - + -
158A LEU* 3.4 45.1 - - + -
161A ALA* 3.9 15.5 - - + +
162A GLU* 6.0 1.1 - - - +
238A ILE* 3.1 35.8 - - + +
242A THR* 4.1 12.3 - - + -
800A ILE* 4.8 4.7 - - + +
837A ARG 3.0 19.1 + - - +
838A TRP* 3.7 29.6 - + - +
840A ARG* 1.3 76.6 - - - +
842A SER* 1.3 61.1 + - - +
844A ALA* 3.0 4.3 + - - +
845A LEU* 2.8 47.6 + - + +
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Residues in contact with SER 842 (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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821A ILE* 6.3 0.7 - - - -
825A PHE* 3.1 36.5 - - - +
838A TRP* 2.9 35.6 + - - -
839A ILE 3.5 5.2 - - - -
841A TYR* 1.3 78.3 - - - +
843A TRP* 1.3 58.1 + - - +
845A LEU* 3.7 7.5 - - - +
846A CYS* 2.8 36.6 + - - +
875A LEU* 3.8 11.0 - - - -
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Residues in contact with TRP 843 (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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12A PHE* 3.9 3.1 - - + -
16A ILE* 3.6 19.3 - - + -
22A GLN* 3.5 22.6 - - - +
27A PHE* 4.0 20.9 - + - -
839A ILE* 3.0 26.8 + - + -
840A ARG* 3.1 8.3 + - - +
842A SER* 1.3 76.9 - - - +
844A ALA* 1.3 58.1 + - - +
846A CYS* 3.8 1.6 - - + +
847A CYS* 2.9 31.5 + - - +
867A MET* 3.5 46.0 - - + -
870A PHE* 4.2 5.8 - - + -
871A VAL* 4.0 14.6 - - + -
875A LEU* 3.4 34.9 - - + +
876A PRO 2.8 28.8 + - - -
877A LEU* 4.3 1.3 - - + -
878A VAL* 3.7 23.6 - - + +
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Residues in contact with ALA 844 (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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12A PHE* 4.1 12.1 - - - -
16A ILE* 4.4 6.1 - - + -
34A PHE* 3.8 4.5 - - + -
157A ALA* 3.6 29.2 - - - +
160A VAL* 4.4 7.2 - - + -
161A ALA* 4.0 12.6 - - + +
840A ARG 3.1 11.1 + - - +
841A TYR 3.0 9.5 + - - +
843A TRP* 1.3 75.5 - - - +
845A LEU* 1.3 65.5 + - - +
847A CYS* 3.3 3.3 + - - +
848A ALA* 2.9 24.3 + - - +
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Residues in contact with LEU 845 (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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153A LYS 4.6 0.9 - - - +
154A PHE* 3.9 27.8 - - + -
157A ALA* 4.0 17.2 - - + +
821A ILE* 3.4 36.6 - - + +
824A VAL* 4.9 12.8 - - + -
841A TYR* 2.8 35.9 + - + +
842A SER* 3.7 8.5 - - - +
844A ALA* 1.3 77.5 - - - +
846A CYS* 1.3 63.0 + - - +
848A ALA* 3.0 12.7 + - + +
849A PHE* 3.3 47.8 + - + -
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Residues in contact with CYS 846 (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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818A LEU* 5.6 0.2 - - - -
821A ILE* 4.1 21.1 - - - +
822A MET* 4.1 11.4 - - - -
825A PHE* 6.2 1.1 - - - -
842A SER* 2.8 29.3 + - - +
843A TRP* 3.8 4.7 - - + +
845A LEU* 1.3 72.9 - - - +
847A CYS* 1.3 62.6 + - - +
849A PHE* 3.0 6.4 + - - +
850A SER* 3.0 23.4 + - - -
870A PHE* 3.2 48.5 - - + -
875A LEU* 3.9 14.8 - - + -
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Residues in contact with CYS 847 (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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12A PHE* 3.8 8.3 - - + -
27A PHE* 3.3 35.2 - - + -
30A ALA* 3.4 20.6 - - - -
31A ALA* 3.3 37.9 - - - +
34A PHE* 3.8 7.9 - - + -
843A TRP 2.9 19.5 + - - +
844A ALA 3.5 4.9 - - - +
846A CYS* 1.3 76.3 - - - +
848A ALA* 1.3 58.6 + - - +
849A PHE 3.1 3.6 + - - -
850A SER* 2.7 18.4 + - - -
851A ARG* 4.6 0.5 + - - +
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Residues in contact with ALA 848 (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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34A PHE* 3.6 37.5 - - + +
35A SER* 5.4 0.7 + - - -
153A LYS* 3.1 41.8 + - + +
157A ALA* 4.9 0.9 - - + -
844A ALA 2.9 13.4 + - - +
845A LEU* 3.0 13.8 + - - +
847A CYS* 1.3 76.3 - - - +
849A PHE* 1.3 64.0 + - + +
851A ARG 5.4 0.8 - - - +
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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
------------------------------------------------------------
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