Contacts of the strand formed by residues 402 - 407 (chain A) in PDB entry 3LX9
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 ARG 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A THR* 3.4 37.6 + - + +
367A ILE* 3.4 4.5 - - - +
368A ALA* 4.2 18.2 - - + +
369A VAL* 4.5 0.2 - - - -
397A TYR* 3.5 17.3 - - - -
400A THR 4.9 4.7 - - - +
401A SER* 1.3 78.9 - - - +
403A LEU* 1.3 60.7 + - - +
404A ARG* 4.0 2.3 + - - +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 6.0 0.4 - - + -
353A MET* 4.5 8.7 - - + +
365A TYR* 3.6 1.6 - - - +
366A THR* 3.2 6.1 - - - +
367A ILE* 2.7 50.7 + - + +
369A VAL* 4.0 12.2 - - + +
372A LEU* 4.6 9.2 - - + -
384A ILE* 4.1 22.9 - - + -
394A LEU* 4.5 12.3 - - + -
397A TYR* 4.0 18.2 - - + +
402A ARG* 1.3 72.3 - - - +
404A ARG* 1.3 83.7 + - - +
405A SER* 3.8 8.9 + - - +
415A LEU* 3.2 31.4 - - + -
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Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER* 3.6 24.1 + - - +
365A TYR 3.4 3.6 - - - -
366A THR* 3.9 21.4 + - + +
394A LEU* 5.8 0.5 - - - +
397A TYR* 5.1 2.6 + - - -
402A ARG 4.0 3.3 + - - +
403A LEU* 1.3 80.6 - - - +
405A SER* 1.3 69.5 + - - +
406A HIS* 3.8 26.0 + - + -
58B GLU* 3.5 39.8 + - - +
59B GLU* 5.2 2.4 + - - +
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Residues in contact with SER 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A MET* 3.2 34.3 - - - +
363A ARG 3.7 0.3 - - - +
364A SER* 3.3 4.5 + - - -
365A TYR 2.7 40.3 + - - -
386A GLN* 5.1 3.2 + - - -
394A LEU* 5.3 2.1 - - - +
403A LEU* 3.8 8.7 - - - +
404A ARG* 1.3 75.6 + - - +
406A HIS* 1.3 67.7 + - - +
407A ILE* 4.2 9.0 - - - -
413A VAL* 4.2 10.6 - - - +
415A LEU* 4.8 2.3 - - - +
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Residues in contact with HIS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PRO* 4.5 19.1 - - + -
363A ARG 3.3 5.6 - - - +
364A SER* 3.8 22.8 - - - -
404A ARG* 3.8 30.3 + - - +
405A SER* 1.3 73.3 - - - +
407A ILE* 1.3 62.5 + - - +
408A ASN* 4.3 1.0 + - - +
413A VAL* 3.8 13.9 - - - +
59B GLU* 3.6 25.3 + - - +
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Residues in contact with ILE 407 (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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337A PHE* 4.1 13.5 - - + -
353A MET* 3.5 44.6 - - + +
354A ILE 4.5 0.4 - - - +
355A ASN* 3.0 35.1 + - + +
362A PRO* 4.1 1.8 - - - -
363A ARG 3.0 24.5 + - - +
365A TYR* 4.0 22.0 - - + -
405A SER* 4.5 3.6 - - - -
406A HIS* 1.3 81.1 - - - +
408A ASN* 1.3 63.3 + - - +
411A GLY 3.5 28.7 - - - +
412A THR* 4.1 3.6 - - - +
413A VAL* 4.0 14.8 - - + +
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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
------------------------------------------------------------
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