Contacts of the helix formed by residues 555 - 569 (chain X) in PDB entry 1T6B
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 555 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322X ALA* 3.3 28.1 - - - +
323X GLY 4.6 0.4 - - - +
324X PHE* 3.6 25.1 - - + -
554X PHE* 1.3 76.1 - - - +
556X GLN* 1.3 64.2 + - - +
557X GLN* 2.9 11.4 + - - +
558X THR* 2.6 45.9 + - - -
559X SER* 2.8 20.6 + - - -
586X LYS 4.0 2.3 - - - +
587X MET 4.0 0.3 - - - -
588X ASN* 2.8 38.6 + - + +
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Residues in contact with GLN 556 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321X SER* 3.8 16.8 + - - +
324X PHE* 4.7 11.3 - - + -
555X ASP* 1.3 73.0 - - - +
557X GLN* 1.3 77.9 + - - +
559X SER* 3.4 7.3 - - - -
560X GLN* 3.3 44.3 + - - +
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Residues in contact with GLN 557 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324X PHE* 4.7 14.5 - - + -
555X ASP* 2.9 11.9 + - - +
556X GLN* 1.3 89.5 - - - +
558X THR* 1.3 64.4 + - - +
559X SER 3.2 1.1 - - - -
560X GLN* 3.5 17.9 + - - +
561X ASN* 3.1 21.7 + - - +
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Residues in contact with THR 558 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554X PHE* 3.8 26.2 - - + -
555X ASP* 2.6 39.7 + - - -
557X GLN* 1.3 73.3 - - - +
559X SER* 1.3 54.2 + - - +
561X ASN* 3.1 7.4 + - - +
562X ILE* 2.8 41.0 + - + +
586X LYS 4.5 0.3 + - - -
587X MET* 3.4 48.6 - - + +
588X ASN 3.4 4.4 + - - +
589X ILE* 4.6 1.3 - - + -
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Residues in contact with SER 559 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321X SER* 5.8 0.7 - - - -
554X PHE* 3.7 25.5 + - - +
555X ASP 2.8 19.3 + - - -
556X GLN* 3.4 9.0 - - - -
558X THR* 1.3 77.0 - - - +
560X GLN* 1.3 63.2 + - - +
562X ILE* 3.3 1.9 + - - +
563X LYS* 3.0 43.0 + - - +
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Residues in contact with GLN 560 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556X GLN* 3.3 30.6 + - - +
557X GLN* 3.7 20.3 + - - +
558X THR 3.4 0.2 - - - -
559X SER* 1.3 74.4 - - - +
561X ASN* 1.3 67.2 + - - +
563X LYS* 3.3 16.4 + - - +
564X ASN* 3.0 36.3 + - - +
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Residues in contact with ASN 561 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557X GLN 3.1 10.5 + - - +
558X THR* 3.1 12.7 + - - +
560X GLN* 1.3 80.7 - - - +
562X ILE* 1.3 61.7 + - - +
564X ASN* 3.1 7.8 + - - +
565X GLN* 2.7 52.1 + - - +
584X ASN* 3.4 23.2 + - - +
587X MET* 3.6 13.0 - - + +
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Residues in contact with ILE 562 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523X LEU* 5.4 1.3 - - + -
554X PHE* 4.0 34.1 - - + -
558X THR* 2.8 29.9 + - + +
559X SER 3.7 4.3 - - - +
561X ASN* 1.3 72.1 + - - +
563X LYS* 1.3 64.3 + - - +
565X GLN* 3.1 15.3 + - - +
566X LEU* 3.0 32.6 + - + +
574X ILE* 3.9 26.7 - - + -
581X ILE* 3.9 26.0 - - + -
582X LYS 4.9 0.4 - - - +
583X LEU* 5.5 1.3 - - + -
587X MET* 4.3 16.8 - - + -
589X ILE* 5.4 2.9 - - + -
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Residues in contact with LYS 563 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559X SER* 3.0 37.0 + - - +
560X GLN* 3.6 16.9 - - - +
562X ILE* 1.3 77.8 - - - +
564X ASN* 1.3 61.6 + - - +
566X LEU* 3.4 15.3 + - + +
567X ALA* 3.2 26.2 + - - +
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Residues in contact with ASN 564 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560X GLN* 3.0 26.3 + - - +
561X ASN* 3.6 9.5 - - - +
562X ILE 3.1 0.2 - - - -
563X LYS* 1.3 79.8 - - - +
565X GLN* 1.3 68.1 + - + +
567X ALA* 3.4 7.7 + - - +
568X GLU* 3.0 31.4 + - - +
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Residues in contact with GLN 565 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561X ASN* 2.7 35.4 + - - +
562X ILE* 3.3 16.4 - - - +
564X ASN* 1.3 80.5 - - + +
566X LEU* 1.3 56.4 + - - +
568X GLU* 3.5 7.0 - - - +
569X LEU* 3.0 35.9 + - + +
580X LYS 4.2 1.7 - - - +
581X ILE* 3.4 19.2 - - + -
582X LYS* 2.7 56.4 + - - +
584X ASN* 5.5 0.8 + - - -
587X MET* 4.3 2.4 - - - +
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Residues in contact with LEU 566 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562X ILE* 3.0 28.3 + - + +
563X LYS* 3.6 16.4 - - + +
564X ASN 3.1 0.2 - - - -
565X GLN* 1.3 74.6 - - - +
567X ALA* 1.3 59.4 + - - +
569X LEU* 3.0 5.1 + - - -
570X ASN 2.9 8.5 + - - -
571X ALA* 2.8 47.4 + - + +
572X THR 5.2 7.0 - - - +
573X ASN 4.7 0.2 - - - -
574X ILE* 4.2 25.8 - - + +
577X VAL* 3.6 31.0 - - + -
581X ILE* 3.7 12.8 - - + -
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Residues in contact with ALA 567 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563X LYS 3.2 14.0 + - - +
564X ASN* 3.7 8.7 - - - +
566X LEU* 1.3 77.5 - - - +
568X GLU* 1.3 57.5 + - - +
570X ASN* 2.9 26.6 + - - +
571X ALA 5.0 1.6 - - - -
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Residues in contact with GLU 568 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564X ASN* 3.0 23.5 + - - +
565X GLN* 3.5 9.2 - - - +
567X ALA* 1.3 75.3 - - - +
569X LEU* 1.3 59.7 + - + +
570X ASN* 3.7 5.4 + - - -
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Residues in contact with LEU 569 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565X GLN* 3.0 19.0 + - + +
566X LEU* 3.0 10.3 + - - +
568X GLU* 1.3 77.2 - - + +
570X ASN* 1.3 68.9 + - - +
571X ALA* 3.3 9.1 + - + +
577X VAL* 4.0 15.7 - - + +
580X LYS* 3.9 46.2 - - + +
581X ILE* 4.0 22.4 - - + -
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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