Contacts of the helix formed by residues 713 - 726 (chain B) in PDB entry 1N1M
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 PHE 713 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TYR* 3.5 26.5 - + + +
706A THR* 5.1 7.0 - - + -
713A PHE* 6.1 4.0 - + - -
734A TRP* 3.7 48.7 - + + -
238B TYR* 6.1 2.9 - - + -
704B HIS* 3.7 38.2 + - + -
705B GLY 3.6 21.1 - - - +
706B THR* 3.8 28.4 + - + +
708B ASP* 4.3 5.1 + - - +
711B VAL 3.6 1.2 + - - -
712B HIS* 1.3 71.1 - - - +
714B GLN* 1.3 64.8 + - - +
716B SER* 2.9 7.3 + - - -
717B ALA* 2.9 25.0 + - + -
734B TRP* 4.1 14.1 - - + -
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Residues in contact with GLN 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TYR* 3.5 33.2 + - + -
246A LEU 3.6 6.9 + - - -
247A GLN 2.7 26.6 + - - -
248A TYR 4.3 0.2 - - - -
249A PRO* 3.6 26.3 - - + +
258B LYS* 3.0 26.5 + - - -
661B TYR* 3.5 33.7 - - + +
712B HIS* 2.9 10.9 - - + +
713B PHE* 1.3 77.3 - - - +
715B GLN* 1.3 55.5 + - - +
717B ALA* 3.0 3.3 + - - +
718B GLN* 2.8 36.3 + - + +
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Residues in contact with GLN 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B PRO 3.7 15.5 - - - +
656B VAL* 3.5 13.2 - - - +
657B SER* 2.8 59.2 + - - +
658B ARG 3.5 4.5 + - - +
661B TYR* 3.3 49.4 + - + +
662B TYR* 3.8 11.7 - - - +
704B HIS* 4.7 0.2 - - + -
710B ASN 5.2 0.4 + - - -
711B VAL* 4.1 16.7 - - + +
712B HIS* 2.9 18.4 + - + +
714B GLN* 1.3 82.1 - - - +
716B SER* 1.3 58.7 + - - +
718B GLN* 3.5 1.2 + - - +
719B ILE* 3.3 12.9 + - - +
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Residues in contact with SER 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A TRP* 3.8 9.1 - - - -
655B PRO* 3.6 8.3 - - - +
702B LEU* 3.3 32.8 - - - +
704B HIS* 2.4 38.9 + - - -
713B PHE* 2.9 8.3 + - - -
715B GLN* 1.3 73.0 - - - +
717B ALA* 1.3 61.3 + - - +
718B GLN 3.2 0.7 - - - -
719B ILE* 3.1 10.7 + - - +
720B SER* 2.9 29.3 + - - -
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Residues in contact with ALA 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 4.0 31.9 - - + -
734A TRP* 4.1 6.0 - - - +
736A THR* 2.8 32.8 + - - +
713B PHE* 2.9 20.2 + - + +
714B GLN* 3.0 15.9 + - - +
716B SER* 1.3 78.2 - - - +
718B GLN* 1.3 57.5 + - - +
720B SER* 2.9 9.9 + - - -
721B LYS* 3.1 7.4 + - - +
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Residues in contact with GLN 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.6 15.2 - - + +
242A SER 2.9 18.9 - - - +
243A ASP 3.5 7.6 - - - +
244A GLU* 3.6 13.3 - - + +
246A LEU 5.1 1.6 - - - +
661B TYR* 3.2 26.8 + - + +
689B MET* 3.7 25.6 - - + +
714B GLN* 2.8 23.8 + - + +
715B GLN 3.9 2.0 - - - +
716B SER 3.2 0.2 - - - -
717B ALA* 1.3 75.2 - - - +
719B ILE* 1.3 60.7 + - - +
721B LYS* 2.8 31.8 - - - +
722B ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B SER* 4.5 0.7 - - - +
655B PRO* 4.1 21.5 - - + -
657B SER* 3.6 22.0 - - - -
688B VAL* 3.8 30.7 - - + -
689B MET* 4.0 9.9 - - - +
695B PHE* 5.7 0.7 - - + -
700B TYR* 3.9 28.9 - - + +
702B LEU* 3.8 15.0 - - + -
715B GLN 3.3 13.6 + - - +
716B SER* 3.1 10.8 + - - +
718B GLN* 1.3 76.0 - - - +
720B SER* 1.3 66.1 + - - +
722B ALA* 3.4 3.3 + - - +
723B LEU* 3.2 28.8 + - + +
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Residues in contact with SER 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A TRP* 3.0 29.7 + - - -
735A TYR* 6.2 0.2 - - - -
736A THR* 2.8 32.9 - - - +
702B LEU* 4.1 2.2 - - - +
716B SER 2.9 11.9 + - - -
717B ALA 2.9 5.0 + - - -
719B ILE* 1.3 77.6 - - - +
721B LYS* 1.3 59.8 + - - +
723B LEU* 3.1 4.3 + - - +
724B VAL* 3.0 29.1 + - - +
730B PHE* 3.8 27.4 - - - -
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Residues in contact with LYS 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TYR* 5.0 0.4 - - - -
242A SER 2.9 25.6 + - - -
243A ASP* 3.8 9.3 + - - +
244A GLU 4.0 1.0 - - - +
736A THR* 3.5 34.3 - - + +
737A ASP* 3.8 12.6 - - + +
717B ALA 3.1 11.5 + - - +
718B GLN* 2.8 35.2 - - - +
720B SER* 1.3 82.4 + - - +
722B ALA* 1.3 57.1 + - - +
724B VAL* 3.5 7.5 + - + +
725B ASP* 2.9 46.3 + - - +
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Residues in contact with ALA 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 5.6 0.2 - - - +
689B MET* 3.5 31.9 - - + +
692B ALA* 3.8 11.4 - - + +
718B GLN 3.0 18.1 + - - +
719B ILE 3.9 3.6 - - - +
720B SER 3.2 0.4 - - - -
721B LYS* 1.3 74.1 - - - +
723B LEU* 1.3 66.5 + - - +
725B ASP* 3.2 19.7 + - - +
726B VAL* 3.2 16.6 + - - +
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Residues in contact with LEU 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B ALA* 3.7 13.5 - - + +
695B PHE* 3.5 33.7 - - + -
700B TYR* 3.8 26.5 - - + -
719B ILE* 3.2 21.1 + - + +
720B SER 3.1 6.5 + - - +
722B ALA* 1.3 75.7 - - - +
724B VAL* 1.3 63.1 + - - +
726B VAL* 3.3 1.5 + - - -
727B GLY 3.1 3.8 + - - -
728B VAL* 2.8 52.1 + - + +
730B PHE* 3.6 39.9 - - + -
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Residues in contact with VAL 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A MET* 6.1 0.2 - - - -
734A TRP 5.9 0.4 - - - +
735A TYR* 3.9 15.3 - - + -
736A THR* 6.5 0.2 - - + -
746A THR* 3.7 40.2 - - - +
747A ALA* 3.8 13.2 - - + +
750A HIS* 3.8 36.6 - - + +
720B SER* 3.0 22.7 + - - +
721B LYS* 3.6 8.5 - - + +
723B LEU* 1.3 77.6 - - - +
725B ASP* 1.3 66.2 + - - +
727B GLY* 2.9 14.9 + - - -
730B PHE* 4.4 4.0 - - + -
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Residues in contact with ASP 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A THR* 3.7 32.4 + - + +
721B LYS* 2.9 36.7 + - - +
722B ALA* 3.2 11.6 + - - +
724B VAL* 1.3 79.0 - - - +
726B VAL* 1.3 62.0 + - + +
727B GLY 3.3 0.7 + - - -
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Residues in contact with VAL 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B ALA* 3.7 25.4 - - + +
693B GLU* 4.0 26.1 - - + +
696B LYS* 4.7 11.4 + - + +
722B ALA 3.4 12.8 - - - +
723B LEU 3.3 1.6 - - - +
724B VAL 3.1 0.2 - - - -
725B ASP* 1.3 81.7 - - + +
727B GLY* 1.3 62.0 + - - +
728B VAL* 3.3 28.8 - - + +
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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
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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