Contacts of the helix formed by residues 548 - 564 (chain A) in PDB entry 3T6A
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 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A ASN 4.2 0.4 + - - -
547A ASN* 1.3 75.2 + - - +
549A PRO* 1.4 69.8 - - - +
550A LYS* 2.7 38.5 + - - +
551A VAL* 3.0 36.1 + - + +
552A ILE* 3.0 12.4 + - - +
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Residues in contact with PRO 549 (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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547A ASN 3.7 0.4 - - - -
548A ASP* 1.4 95.2 - - - +
550A LYS* 1.3 55.4 + - - +
552A ILE* 3.5 5.6 + - + +
553A ALA* 3.0 28.1 + - - +
629A LYS* 3.8 27.1 - - + -
632A GLN* 4.1 21.8 - - + +
633A VAL* 3.9 34.1 - - + +
636A GLU* 3.9 10.2 - - + +
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Residues in contact with LYS 550 (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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548A ASP* 2.7 20.2 + - - +
549A PRO* 1.3 74.8 - - - +
551A VAL* 1.3 58.3 + - + +
553A ALA* 3.1 2.9 + - - +
554A GLN* 2.9 58.6 + - + +
636A GLU* 2.8 45.7 + - - +
640A SER* 3.2 21.2 + - - -
641A MET* 4.3 5.3 - - + +
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Residues in contact with VAL 551 (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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547A ASN* 4.0 19.5 - - - +
548A ASP* 3.0 29.0 + - + +
550A LYS* 1.3 77.0 - - + +
552A ILE* 1.3 64.2 + - - +
554A GLN* 3.4 16.8 + - - +
555A HIS* 2.9 50.1 + - + +
768A PHE* 5.6 0.4 - - + -
771A ASP* 6.1 1.3 - - + -
774A MET* 4.8 2.2 - - + -
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Residues in contact with ILE 552 (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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544A PHE* 3.5 51.4 - - + +
547A ASN* 3.6 24.5 - - + +
548A ASP 3.0 13.0 + - - +
549A PRO* 3.7 8.1 - - + +
551A VAL* 1.3 76.3 - - - +
553A ALA* 1.3 62.1 + - - +
555A HIS* 3.2 5.9 + - - +
556A VAL* 3.1 30.0 + - + +
629A LYS* 4.3 2.0 - - - -
633A VAL* 4.0 29.2 - - + -
774A MET* 4.7 17.5 - - - -
778A CYS* 5.1 1.1 - - - -
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Residues in contact with ALA 553 (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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549A PRO 3.0 18.1 + - - +
550A LYS* 3.1 4.7 + - - +
552A ILE* 1.3 78.0 - - - +
554A GLN* 1.3 57.4 + - - +
556A VAL* 4.4 1.6 - - - -
557A LEU* 3.0 31.5 + - - +
633A VAL* 4.5 2.5 - - + +
636A GLU* 3.7 19.1 - - + -
637A LEU* 3.7 21.7 - - + +
641A MET* 3.5 21.9 - - + +
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Residues in contact with GLN 554 (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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550A LYS* 2.9 38.6 + - - +
551A VAL* 3.6 21.2 - - - +
552A ILE 3.3 0.2 - - - -
553A ALA* 1.3 75.9 - - - +
555A HIS* 1.3 57.9 + - - +
557A LEU* 4.0 0.9 - - - +
558A SER* 3.0 31.5 + - - -
641A MET* 3.8 24.1 - - + +
764A ILE 5.3 6.2 + - - +
765A LEU* 4.2 11.0 - - + +
768A PHE* 3.5 38.0 - - + +
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Residues in contact with HIS 555 (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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551A VAL* 2.9 34.1 + - + -
552A ILE 3.2 7.9 + - - +
554A GLN* 1.3 75.3 - - - +
556A VAL* 1.3 64.7 + - - +
558A SER* 3.7 3.2 - - - -
559A MET* 3.0 26.0 + - - +
768A PHE* 3.5 25.8 - + - -
769A GLN 4.9 1.1 - - - -
770A PRO* 3.5 5.6 - - + +
771A ASP* 2.8 34.9 + - + -
774A MET* 3.0 40.1 - - + +
775A ASN* 3.6 22.4 + - + +
778A CYS* 3.7 13.6 - - - +
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Residues in contact with VAL 556 (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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552A ILE* 3.1 27.2 + - + +
553A ALA* 3.9 5.4 - - - +
555A HIS* 1.3 75.7 - - - +
557A LEU* 1.3 53.9 + - - +
559A MET* 3.1 4.8 + - - +
560A ASP* 2.7 41.1 + - - +
601A ARG* 4.6 5.8 - - - +
605A MET* 4.7 7.9 - - + -
633A VAL* 5.7 1.1 - - + -
637A LEU* 4.0 16.4 - - + -
646A SER* 3.3 37.9 - - - +
650A LEU* 6.2 0.9 - - + -
778A CYS* 4.3 14.8 - - - -
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Residues in contact with LEU 557 (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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553A ALA 3.0 17.7 + - - +
554A GLN 4.0 2.5 - - - +
556A VAL* 1.3 77.5 - - - +
558A SER* 1.3 57.4 + - - +
560A ASP* 3.3 0.9 + - - +
561A CYS* 2.9 45.2 + - - -
637A LEU* 4.7 0.2 - - - +
641A MET* 3.5 46.0 - - + +
643A ASP* 3.4 14.1 + - + +
706A SER* 3.9 14.4 - - - +
707A VAL* 3.9 16.8 - - + -
761A ALA* 4.7 2.2 - - + +
764A ILE* 3.9 16.4 - - + -
765A LEU* 4.1 17.9 - - + -
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Residues in contact with SER 558 (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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554A GLN 3.0 21.9 + - - -
555A HIS* 3.7 4.7 + - - -
557A LEU* 1.3 77.5 - - - +
559A MET* 1.3 61.1 + - - +
561A CYS* 3.5 5.7 + - - +
562A ARG* 3.3 41.1 + - - +
567A LEU* 5.7 1.0 - - - +
765A LEU* 3.9 20.0 - - - -
768A PHE* 4.0 20.6 - - - -
770A PRO* 5.7 0.3 - - - +
775A ASN* 4.6 5.0 + - - -
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Residues in contact with MET 559 (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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515A PHE* 5.8 3.1 - - + -
555A HIS 3.0 18.6 + - - +
556A VAL 3.6 0.2 - - - +
558A SER* 1.3 73.4 + - - +
560A ASP* 1.3 64.6 + - - +
561A CYS 3.1 1.1 - - - -
562A ARG* 3.1 36.9 + - + +
563A VAL* 3.0 38.1 + - + +
601A ARG* 3.3 33.2 - - - +
775A ASN* 5.1 2.2 - - - +
778A CYS* 3.5 15.5 - - + +
779A LYS* 3.5 42.2 - - + -
780A THR* 4.2 2.7 - - - +
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Residues in contact with ASP 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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556A VAL* 2.7 19.7 + - - +
557A LEU 3.7 1.8 - - - +
559A MET* 1.3 71.1 - - - +
561A CYS* 1.3 59.4 + - - +
563A VAL* 4.1 2.2 - - - +
564A ALA* 2.9 34.1 + - - +
601A ARG* 2.8 34.5 + - - +
643A ASP* 2.4 33.1 - - - +
645A TYR* 3.7 15.6 - - + -
646A SER* 2.4 26.5 + - - -
707A VAL* 4.3 12.1 - - + -
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Residues in contact with CYS 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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557A LEU* 2.9 40.9 + - - +
558A SER* 3.8 6.7 - - - +
559A MET 3.1 0.4 - - - -
560A ASP* 1.3 77.4 - - - +
562A ARG* 1.3 60.6 + - - +
565A ARG* 3.2 1.0 + - - -
566A ILE* 2.8 41.2 + - - -
567A LEU* 3.1 30.8 + - + +
707A VAL* 4.1 10.3 - - - -
761A ALA* 3.7 24.0 - - - -
765A LEU* 5.2 0.2 - - - -
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Residues in contact with ARG 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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558A SER* 3.3 29.9 + - - +
559A MET* 3.1 38.0 + - - +
561A CYS* 1.3 79.1 - - - +
563A VAL* 1.3 63.9 + - + +
565A ARG* 3.0 20.1 + - - +
567A LEU* 3.9 17.5 - - + +
568A GLY* 5.4 4.7 - - - -
770A PRO* 6.3 0.6 - - - +
775A ASN* 3.2 36.0 + - - +
779A LYS* 5.0 4.6 - - - +
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Residues in contact with VAL 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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515A PHE* 4.3 24.5 - - + -
559A MET* 3.0 41.4 + - + +
560A ASP* 4.1 3.6 - - - +
562A ARG* 1.3 77.6 - - + +
564A ALA* 1.3 61.3 + - + +
565A ARG* 3.1 6.6 + - - +
594A LEU* 3.5 15.4 - - - +
597A ASP* 5.0 11.0 - - + -
598A ILE* 5.0 11.0 - - + -
601A ARG* 4.0 29.6 - - + +
645A TYR* 5.6 2.0 - - + +
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Residues in contact with ALA 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 ASP 2.9 17.1 + - - +
563A VAL* 1.3 77.0 - - + +
565A ARG* 1.3 69.5 + - - +
566A ILE* 3.4 19.4 + - + +
582A GLY* 3.2 20.6 + - - -
583A LEU* 4.0 10.9 + - + -
594A LEU* 4.4 9.8 - - - +
598A ILE* 5.0 8.5 - - + -
645A TYR* 6.4 1.8 - - + -
707A VAL* 5.0 3.8 - - + -
710A LEU* 4.7 15.0 - - + -
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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