Contacts of the helix formed by residues 614 - 622 (chain A) in PDB entry 6TAV
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 614 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612A GLU* 2.7 29.8 + - - -
613A LEU* 1.3 74.8 - - - +
615A ALA* 1.4 64.7 + - - +
616A SER* 3.4 7.2 + - - -
617A SER* 3.1 19.3 + - - -
618A VAL* 3.1 18.1 + - - +
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Residues in contact with ALA 615 (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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562A ASN 4.0 19.5 - - - +
563A CYS* 5.0 0.7 - - - -
564A LEU* 3.4 31.9 - - + -
614A SER* 1.4 72.6 - - - +
616A SER* 1.3 59.3 - - - +
618A VAL* 2.9 9.3 + - - +
619A TYR* 2.9 32.8 + - + -
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Residues in contact with SER 616 (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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562A ASN* 4.2 26.6 + - - +
612A GLU* 4.2 6.5 - - - -
614A SER* 3.3 10.4 + - - -
615A ALA* 1.3 78.3 - - - +
617A SER* 1.4 55.8 + - - +
619A TYR* 4.0 1.9 - - - +
620A ASN* 2.7 39.1 + - - -
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Residues in contact with SER 617 (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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612A GLU* 3.0 30.8 + - - -
613A LEU* 4.0 7.6 - - - +
614A SER* 3.1 32.8 + - - -
616A SER* 1.4 75.7 - - - +
618A VAL* 1.3 62.2 + - - +
620A ASN* 3.7 6.9 + - - +
621A LEU* 3.6 17.7 + - - +
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Residues in contact with VAL 618 (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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128A LEU* 5.2 0.2 - - + -
130A PHE* 4.8 16.4 - - + -
151A MET* 4.7 12.3 - - + -
155A PHE* 3.2 36.0 - - + -
564A LEU* 5.3 9.4 - - + -
613A LEU* 4.2 18.4 - - + -
614A SER 3.1 11.4 + - - +
615A ALA* 2.9 10.8 + - - +
617A SER* 1.3 75.5 - - - +
619A TYR* 1.3 66.7 + - + +
621A LEU* 3.0 26.4 + - + +
622A LEU 3.5 3.6 + - - -
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Residues in contact with TYR 619 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A PHE* 3.7 33.2 - + - -
502A LYS* 5.5 0.9 + - - -
532A SER* 4.2 12.3 + - - -
534A ILE 4.6 1.6 + - - -
535A ALA* 4.0 13.9 - - + -
536A PRO* 3.6 36.7 - - + +
561A GLU 5.0 0.7 + - - -
562A ASN* 3.5 32.3 - - + +
563A CYS* 2.7 50.0 + - - -
564A LEU* 4.3 8.5 - - + -
615A ALA* 2.9 23.2 + - + +
616A SER 4.2 2.2 - - - +
617A SER 3.5 0.2 - - - -
618A VAL* 1.3 77.2 - - + +
620A ASN* 1.3 56.2 + - - +
622A LEU* 3.1 29.1 + - + +
625A LYS* 4.2 11.2 - - - +
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Residues in contact with ASN 620 (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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562A ASN* 5.8 2.0 - - - +
616A SER* 2.7 28.1 + - - +
617A SER* 4.0 7.0 - - - +
618A VAL 3.2 1.0 - - - -
619A TYR* 1.3 76.7 - - - +
621A LEU* 1.3 60.7 + - - +
622A LEU 3.4 5.9 + - - +
625A LYS* 2.9 37.4 + - - +
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Residues in contact with LEU 621 (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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128A LEU* 3.6 23.9 - - + +
129A VAL 3.2 43.3 - - - +
130A PHE* 4.2 19.7 - - + -
151A MET* 4.7 2.9 - - + -
215A THR* 4.7 10.8 - - + -
617A SER 3.6 11.4 + - - +
618A VAL* 3.0 19.4 + - + +
620A ASN* 1.3 78.1 - - - +
622A LEU* 1.3 59.5 + - - +
623A PRO* 3.5 4.7 - - - +
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Residues in contact with LEU 622 (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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128A LEU* 3.6 10.7 - - + +
153A GLU* 3.5 33.2 - - + +
155A PHE* 3.5 28.9 - - + -
502A LYS* 3.9 19.7 - - + -
535A ALA* 5.2 4.0 - - + -
536A PRO* 5.8 1.6 - - + -
618A VAL 3.5 1.6 + - - -
619A TYR* 3.1 19.8 + - + +
620A ASN 4.0 3.9 - - - +
621A LEU* 1.3 76.7 - - - +
623A PRO* 1.4 86.7 - - + +
624A GLU 3.8 14.1 - - - +
625A LYS* 3.3 31.4 - - + +
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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