Contacts of the strand formed by residues 549 - 555 (chain A) in PDB entry 3P4P
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.7 9.1 - - - +
525A ARG* 2.4 34.8 + - - +
546A ASN* 2.9 27.4 + - - +
547A PHE* 2.8 20.6 + - + +
548A LEU* 1.3 77.0 - - - +
550A HIS* 1.3 50.6 + - - +
565A TYR* 3.9 40.5 - - + +
566A SER 2.7 24.2 - - - +
567A ASP* 4.5 6.5 - - - +
568A VAL* 3.7 5.8 - - - -
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Residues in contact with HIS 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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76A LEU* 2.9 32.0 + - - +
78A GLU* 2.7 37.9 + - + +
224A ARG* 3.7 28.1 + - - -
225A ASP* 2.6 31.5 + - - +
384A GLY* 5.1 4.0 - - - -
387A GLY* 5.4 0.7 - - - -
525A ARG* 4.1 0.2 - - - +
549A LYS* 1.3 72.8 - - - +
551A THR* 1.3 61.5 + - - +
552A LEU* 3.6 0.4 + - + -
565A TYR* 3.4 6.8 - - - -
566A SER* 2.7 52.3 + - - +
567A ASP 3.7 10.8 - - - -
568A VAL* 3.6 5.9 - - + +
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Residues in contact with THR 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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223A LEU 4.2 0.2 - - - +
224A ARG* 3.4 3.8 - - - +
225A ASP* 2.8 34.2 + - - +
227A GLU* 2.6 34.1 + - - -
521A SER* 3.1 30.7 + - - +
525A ARG* 3.6 10.7 + - - +
550A HIS* 1.3 71.7 - - - +
552A LEU* 1.3 64.0 + - - +
563A LEU* 4.0 21.1 - - + -
564A GLU 4.5 0.7 - - - +
565A TYR* 3.6 23.3 + - + +
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Residues in contact with LEU 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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222A PRO* 4.2 8.5 - - + -
223A LEU 3.7 1.1 - - - -
224A ARG* 3.7 29.2 - - + -
362A GLU* 3.6 28.0 - - - +
370A ARG* 3.9 18.2 - - - +
550A HIS 4.2 1.6 - - - +
551A THR* 1.3 83.0 - - - +
553A ALA* 1.3 60.8 + - - +
554A PHE* 4.0 15.9 + - + -
562A ARG 3.7 0.2 - - - +
563A LEU* 3.1 6.8 - - - +
564A GLU* 2.8 52.3 + - + +
565A TYR 4.8 0.9 - - - +
566A SER* 4.1 24.9 - - - +
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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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217A LEU* 3.5 8.1 - - - +
222A PRO* 3.1 6.0 - - - +
223A LEU* 2.8 37.2 + - + +
226A MET* 5.2 1.8 - - + -
517A CYS* 3.9 30.1 - - + -
521A SER* 4.2 8.3 - - - +
551A THR 4.2 0.2 - - - -
552A LEU* 1.3 73.0 - - - +
554A PHE* 1.3 60.8 + - - +
561A THR* 4.6 1.8 - - + -
562A ARG 3.4 4.0 - - - +
563A LEU* 3.9 17.5 - - + -
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Residues in contact with PHE 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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217A LEU* 4.3 2.2 - - - -
220A GLY* 3.6 21.5 - - - -
221A VAL 5.2 0.4 - - - -
222A PRO* 3.5 31.6 - - + -
370A ARG* 3.5 35.2 - - - -
517A CYS* 5.3 0.4 - - - -
552A LEU* 4.0 12.3 - - + -
553A ALA* 1.3 79.3 - - - +
555A ARG* 1.3 64.1 + - - +
556A ASP* 4.9 6.5 - - - +
561A THR* 3.4 6.1 - - - +
562A ARG* 2.7 45.3 + - + +
564A GLU* 3.5 41.5 - - + -
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Residues in contact with ARG 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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217A LEU* 3.7 49.0 + - + +
218A SER* 5.5 1.0 - - - +
220A GLY* 5.1 6.8 + - - -
483A GLN* 3.2 18.4 + - - +
513A ASN* 3.4 35.2 + - - +
516A GLU* 2.8 29.3 + - - -
517A CYS* 5.1 0.7 - - - -
554A PHE* 1.3 77.1 - - - +
556A ASP* 1.3 69.6 + - - +
559A GLY* 4.0 27.2 + - - -
560A THR 3.2 9.0 - - - +
561A THR* 4.5 11.0 + - - +
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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