Contacts of the helix formed by residues 551 - 565 (chain A) in PDB entry 3L2P
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 LYS 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A MET* 4.3 4.5 - - - -
549A VAL* 4.2 3.1 - - - +
550A THR* 1.3 89.9 - - + +
552A ALA* 1.3 90.2 + - - +
553A LEU* 4.0 21.9 - - + +
554A ASP* 3.0 25.1 + - + +
555A LEU 3.5 3.8 + - - -
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Residues in contact with ALA 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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405A VAL* 3.8 14.9 - - + +
409A MET* 3.7 31.1 - - + +
551A LYS* 1.3 87.5 - - - +
553A LEU* 1.3 64.4 + - + +
555A LEU* 3.2 5.6 + - - +
556A ALA* 3.0 23.5 + - - +
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Residues in contact with LEU 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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551A LYS* 3.1 19.0 + - + +
552A ALA* 1.3 78.1 - - + +
554A ASP* 1.3 64.1 + - - +
556A ALA* 3.3 8.1 + - + +
557A ASP* 3.1 23.4 + - - +
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Residues in contact with ASP 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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548A ARG 4.9 3.5 - - - +
549A VAL* 4.5 18.0 - - + +
550A THR* 5.4 4.9 - - + +
551A LYS* 3.0 19.3 + - + +
553A LEU* 1.3 78.7 - - - +
555A LEU* 1.3 61.4 + - - +
557A ASP* 3.7 8.0 - - - +
558A MET* 3.6 23.2 + - - +
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Residues in contact with LEU 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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405A VAL* 4.0 21.1 - - + -
408A ALA* 4.3 12.1 - - + -
409A MET* 4.6 5.4 - - - -
416A MET* 3.4 39.0 - - + -
418A SER* 6.2 0.2 - - - -
549A VAL* 3.6 19.2 - - + +
551A LYS 3.5 2.5 + - - +
552A ALA* 3.2 11.3 + - - +
554A ASP* 1.3 75.1 - - - +
556A ALA* 1.3 53.6 + - - +
557A ASP 3.0 5.2 - - - -
558A MET* 2.8 29.0 + - + +
559A ILE* 3.0 41.7 + - + +
570A LEU* 5.1 2.7 - - + -
572A LEU* 4.4 16.2 - - + -
589A VAL* 5.6 0.2 - - + -
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Residues in contact with ALA 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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405A VAL* 4.1 18.8 - - + -
552A ALA 3.0 15.4 + - - +
553A LEU* 3.3 9.8 + - + +
555A LEU* 1.3 78.6 - - - +
557A ASP* 1.3 60.5 + - - +
559A ILE* 3.8 12.3 + - - +
560A THR* 3.2 24.8 + - - +
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Residues in contact with ASP 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 LEU 3.1 15.8 + - - +
554A ASP* 3.7 9.2 - - - +
555A LEU 3.0 0.2 - - - -
556A ALA* 1.3 77.9 - - - +
558A MET* 1.3 54.4 + - - +
560A THR* 2.5 24.2 + - - -
561A ARG* 2.6 54.7 + - - +
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Residues in contact with MET 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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418A SER* 2.9 31.4 - - - -
547A LYS* 4.3 26.0 - - + -
549A VAL* 3.3 31.0 - - + -
554A ASP* 3.6 13.3 + - - +
555A LEU* 2.8 11.7 + - - +
557A ASP* 1.3 76.7 - - - +
559A ILE* 1.3 65.3 + - - +
561A ARG* 3.3 28.2 + - - +
562A VAL* 2.9 32.6 + - + +
570A LEU* 3.8 16.6 - - + -
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Residues in contact with ILE 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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405A VAL* 5.4 6.7 - - + -
555A LEU* 3.0 38.1 + - + +
556A ALA* 3.8 12.1 - - - +
558A MET* 1.3 75.0 - - - +
560A THR* 1.3 64.6 + - + +
562A VAL* 3.7 2.8 - - - +
563A ILE* 2.9 41.0 + - + +
570A LEU* 4.4 13.6 - - + +
589A VAL* 3.7 38.4 - - + -
590A LYS* 6.1 0.4 - - - -
591A LYS* 6.0 2.5 - - - +
594A LEU* 6.2 4.0 - - + -
599A MET* 6.3 3.1 - - + -
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Residues in contact with THR 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 ALA 3.2 13.7 + - - +
557A ASP* 2.5 27.4 + - - -
559A ILE* 1.3 81.8 - - + +
561A ARG* 1.3 63.0 + - - +
562A VAL 2.8 2.4 + - - -
563A ILE* 3.2 18.1 + - + +
564A GLN* 3.1 29.2 + - - +
599A MET* 5.6 9.2 - - + -
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Residues in contact with ARG 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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547A LYS* 3.0 42.2 - - - +
557A ASP* 2.6 41.7 + - - +
558A MET* 3.6 32.1 - - - +
560A THR* 1.3 71.8 + - - +
562A VAL* 1.3 64.6 + - + +
564A GLN* 3.3 24.8 - - - +
565A GLU* 4.4 2.1 + - - +
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Residues in contact with VAL 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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420A ILE* 4.4 14.8 - - + -
558A MET* 2.9 23.7 + - + +
559A ILE* 4.0 2.9 - - - +
560A THR 2.8 4.4 + - - -
561A ARG* 1.3 79.8 - - + +
563A ILE* 1.3 68.2 + - + +
564A GLN 2.9 1.6 + - - -
565A GLU 3.8 3.6 + - - -
567A LEU* 3.4 48.9 + - + +
569A GLY* 4.0 25.1 - - - +
570A LEU* 4.3 18.6 - - + -
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Residues in contact with ILE 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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559A ILE* 2.9 32.4 + - + +
560A THR* 3.2 23.8 - - + +
562A VAL* 1.3 78.4 - - + +
564A GLN* 1.3 79.1 + - - +
566A GLY* 3.0 15.9 + - - -
567A LEU 4.6 5.6 - - - -
590A LYS* 6.2 0.2 - - - -
591A LYS* 4.1 33.9 - - + +
599A MET* 4.5 22.4 - - + -
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Residues in contact with GLN 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 THR* 3.1 27.9 + - - +
561A ARG* 3.3 18.4 - - - +
562A VAL 2.9 2.0 - - - -
563A ILE* 1.3 96.7 - - - +
565A GLU* 1.3 61.1 + - + +
566A GLY 3.4 1.6 + - - -
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Residues in contact with GLU 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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561A ARG 4.4 2.0 + - - +
562A VAL 3.8 3.8 + - - -
563A ILE 3.4 0.4 - - - -
564A GLN* 1.3 77.2 - - + +
566A GLY* 1.3 52.0 + - - +
567A LEU* 2.7 30.0 + - + +
746A LYS 5.2 5.5 - - - +
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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