Contacts of the helix formed by residues 559 - 567 (chain A) in PDB entry 1T9A
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 GLU 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PRO* 3.4 10.0 - - - +
137A LYS 3.1 11.6 + - - -
138A HIS* 3.2 36.2 + - - +
141A GLY* 3.6 15.9 - - - -
145A MET* 3.5 6.5 - - + +
529A LEU* 3.9 15.3 - - + -
530A PRO* 4.6 6.5 - - + -
533A ILE* 3.4 14.1 - - + +
556A THR* 3.0 25.5 + - + +
558A THR* 1.3 82.7 - - + +
560A LEU* 1.3 63.1 + - - +
561A SER 3.2 0.9 - - - -
562A SER* 2.6 45.5 + - - -
563A ALA 3.1 5.2 + - - -
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Residues in contact with LEU 560 (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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529A LEU* 3.7 25.9 - - + +
553A PHE* 3.6 26.5 - - + -
557A LEU 3.2 19.3 + - - +
558A THR 3.1 1.6 - - - -
559A GLU* 1.3 77.6 - - - +
561A SER* 1.3 62.2 + - - +
563A ALA* 3.3 20.2 + - + +
564A VAL* 3.4 11.1 + - - +
570A VAL* 6.2 0.2 - - + -
572A ILE* 4.3 7.4 - - + -
608A LEU* 4.2 15.7 - - + -
609A ALA* 4.7 4.7 - - - -
612A MET* 3.6 31.0 - - + -
614A LEU* 3.9 26.6 - - + +
640A LEU* 4.5 8.1 - - + -
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Residues in contact with SER 561 (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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137A LYS* 3.1 29.0 + - - +
558A THR 3.3 13.8 + - - -
560A LEU* 1.3 76.6 - - - +
562A SER* 1.3 60.4 + - - +
564A VAL* 3.2 4.8 + - - +
565A GLN* 2.9 28.8 + - - +
612A MET* 3.8 32.8 - - - -
554B ASN* 4.6 2.8 + - - -
601B LEU* 3.8 15.1 - - - +
602B ASN 5.1 0.2 - - - -
603B PRO* 4.6 8.1 - - - -
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Residues in contact with SER 562 (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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134A VAL* 6.2 0.9 - - - -
135A LEU 4.0 12.3 - - - +
136A PRO* 3.5 10.6 - - - +
137A LYS* 3.6 12.3 + - - +
145A MET* 4.0 15.9 - - - -
533A ILE* 4.4 1.3 - - - -
559A GLU* 2.6 40.7 + - - -
561A SER* 1.3 77.3 + - - +
563A ALA* 1.3 52.0 + - - +
565A GLN* 3.2 7.1 + - - +
566A ALA* 2.7 38.3 + - - +
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Residues in contact with ALA 563 (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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529A LEU* 5.2 1.8 - - + -
533A ILE* 3.7 21.3 - - + +
559A GLU 3.1 3.2 + - - +
560A LEU* 3.4 14.4 - - + +
561A SER 3.2 0.4 - - - -
562A SER* 1.3 79.9 - - - +
564A VAL* 1.3 56.7 + - - +
566A ALA* 3.3 1.5 + - - -
567A GLY* 3.0 22.7 + - - -
568A THR* 3.1 33.5 + - - +
570A VAL* 4.1 16.2 - - + -
614A LEU* 5.9 0.9 - - + -
638A PRO* 4.9 6.5 - - + +
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Residues in contact with VAL 564 (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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560A LEU 3.4 9.4 + - - +
561A SER 3.2 7.1 + - - +
562A SER 3.2 0.2 - - - -
563A ALA* 1.3 76.3 - - + +
565A GLN* 1.3 64.5 + - - +
567A GLY* 3.1 14.3 + - - -
612A MET 3.6 22.4 - - - +
613A GLY* 3.9 17.7 - - - +
614A LEU* 3.9 13.9 - - + -
638A PRO* 4.3 16.2 - - + -
601B LEU* 3.7 17.7 - - + -
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Residues in contact with GLN 565 (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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135A LEU* 4.1 28.1 - - + +
137A LYS* 4.0 10.0 + - - -
561A SER 2.9 15.6 + - - +
562A SER 3.7 4.5 - - - +
564A VAL* 1.3 76.4 - - - +
566A ALA* 1.3 59.7 + - - +
567A GLY 3.6 0.2 + - - -
599B HIS 3.4 23.8 + - - -
600B GLN* 4.0 3.5 - - - +
601B LEU* 3.4 40.9 + - + +
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Residues in contact with ALA 566 (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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134A VAL* 4.3 25.1 - - + -
135A LEU 6.0 0.4 - - - +
533A ILE* 4.7 3.6 - - + -
537A VAL* 5.1 4.0 - - + +
562A SER 2.7 22.0 + - - +
563A ALA* 3.9 4.0 - - - +
564A VAL 3.1 0.2 - - - -
565A GLN* 1.3 73.8 - - - +
567A GLY* 1.3 63.0 + - - +
568A THR* 3.6 19.6 + - + +
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Residues in contact with GLY 567 (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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563A ALA 3.0 4.2 + - - -
564A VAL* 3.1 12.4 + - - -
565A GLN 3.3 0.6 + - - -
566A ALA* 1.3 80.1 - - - +
568A THR* 1.3 59.9 + - - +
569A PRO* 3.3 11.8 - - - +
638A PRO* 6.3 0.7 - - - -
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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