Contacts of the helix formed by residues 355 - 374 (chain F) in PDB entry 4XLN
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 355 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010C THR* 4.0 6.9 - - - +
1011C GLY* 4.7 9.2 + - - -
1013C TYR* 5.2 3.4 - - - -
1064C ASN* 4.7 0.2 - - - -
353F LEU 3.4 4.1 + - - -
354F PRO* 1.3 74.1 - - - +
356F PRO* 1.3 70.5 - - - +
357F VAL* 3.4 15.9 - - - +
358F GLU* 2.7 52.2 + - - +
359F ALA* 3.1 10.2 + - - +
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Residues in contact with PRO 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010C THR* 3.6 14.1 - - + +
1013C TYR* 3.4 35.9 - - + +
1063C ARG* 3.7 29.2 - - + +
1064C ASN* 3.3 32.0 - - - +
1067C TYR* 3.4 22.9 - - + +
354F PRO 3.8 2.2 - - - +
355F SER* 1.3 89.9 - - - +
357F VAL* 1.3 59.3 + - - +
359F ALA* 3.6 13.4 + - - +
360F ALA* 3.7 1.7 + - - +
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Residues in contact with VAL 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010C THR* 4.3 16.4 - - + +
1067C TYR* 3.5 35.5 - - + +
654D LYS* 6.1 0.4 - - - +
671D LYS* 4.9 1.6 + - - -
674D ARG* 3.3 37.5 + - - +
355F SER* 3.4 21.8 - - - +
356F PRO* 1.3 76.4 - - - +
358F GLU* 1.3 66.7 + - + +
360F ALA* 3.6 3.5 + - - +
361F ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F LEU 4.6 1.7 - - - +
354F PRO* 3.5 15.2 - - + +
355F SER* 2.7 49.2 + - - +
357F VAL* 1.3 75.5 - - + +
359F ALA* 1.3 56.7 + - - -
361F ALA* 3.3 8.4 - - - +
362F GLN* 2.9 31.4 + - - +
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Residues in contact with ALA 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064C ASN* 3.9 31.6 - - + +
1068C GLN* 6.1 0.9 - - + -
354F PRO* 5.1 6.0 - - + +
355F SER 3.1 5.8 + - - +
356F PRO 3.7 10.3 - - - +
357F VAL 3.3 0.4 - - - -
358F GLU* 1.3 77.1 - - - +
360F ALA* 1.3 54.4 + - - +
362F GLN* 3.9 3.3 - - - +
363F SER* 2.7 38.7 + - - +
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Residues in contact with ALA 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064C ASN 5.8 0.2 - - - +
1067C TYR* 3.8 33.9 - - + -
1068C GLN* 4.6 23.3 - - + +
1071C ILE* 5.0 10.3 - - + -
1072C LYS* 5.5 1.5 + - - +
356F PRO 3.7 1.4 + - - -
357F VAL 3.6 1.6 + - - -
358F GLU 3.5 0.2 - - - -
359F ALA* 1.3 75.7 - - - +
361F ALA* 1.3 59.6 + - - +
363F SER* 3.7 8.9 - - - -
364F LEU* 2.9 38.1 + - + +
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Residues in contact with ALA 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671D LYS* 3.2 35.0 - - - +
357F VAL 2.9 18.8 + - - +
358F GLU* 3.3 11.7 - - - +
360F ALA* 1.3 74.6 - - - +
362F GLN* 1.3 60.3 + - - +
364F LEU* 3.2 3.8 + - - +
365F LEU* 2.9 29.7 + - - +
436F PHE* 4.1 5.6 - - + -
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Residues in contact with GLN 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768C SER* 5.0 10.3 - - - +
770C GLU* 3.5 24.6 + - + +
358F GLU 2.9 18.1 + - - +
359F ALA* 4.0 3.1 - - - +
361F ALA* 1.3 71.2 - - - +
363F SER* 1.3 62.5 + - - +
365F LEU* 3.4 11.5 + - + +
366F SER* 2.9 37.7 + - - -
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Residues in contact with SER 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068C GLN* 3.8 22.2 + - - -
1072C LYS* 5.1 0.7 - - - -
359F ALA* 2.7 24.9 + - - +
360F ALA* 3.7 5.6 - - - -
362F GLN* 1.3 78.8 - - - +
364F LEU* 1.3 56.1 + - - +
366F SER* 3.2 6.0 + - - -
367F GLU* 2.9 48.7 + - - +
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Residues in contact with LEU 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071C ILE* 4.9 6.1 - - + -
1072C LYS* 5.2 8.5 - - - +
669D ASN* 4.2 20.2 - - + +
670D VAL* 3.5 42.0 - - + +
671D LYS* 3.7 25.6 - - + -
360F ALA* 2.9 24.1 + - + +
361F ALA 3.5 3.8 - - - +
363F SER* 1.3 75.1 - - - +
365F LEU* 1.3 57.3 - - - +
367F GLU* 3.7 13.0 + - + +
368F GLU* 2.9 41.7 + - + +
436F PHE* 4.5 2.7 - - + -
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Residues in contact with LEU 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C SER* 5.4 1.1 - - - +
770C GLU* 4.3 3.8 - - + +
771C GLU* 4.1 36.1 - - + +
774C LEU* 4.0 12.6 - - + -
361F ALA 2.9 16.5 + - - +
362F GLN* 3.7 11.9 - - + +
364F LEU* 1.3 76.1 - - - +
366F SER* 1.3 58.9 + - - +
368F GLU* 4.2 0.2 - - - +
369F LEU* 2.9 54.3 + - + +
433F LEU* 3.8 7.9 - - + -
436F PHE* 3.6 47.5 - - + -
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Residues in contact with SER 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C GLU* 3.8 32.7 + - - +
362F GLN* 2.9 28.7 + - - -
363F SER* 3.8 4.9 - - - -
365F LEU* 1.3 76.1 - - - +
367F GLU* 1.3 60.7 + - - +
369F LEU* 4.3 2.2 - - - +
370F GLU* 3.6 18.4 + - - +
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Residues in contact with GLU 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068C GLN* 4.4 1.7 + - - -
1072C LYS* 3.9 25.0 + - - -
363F SER* 2.9 39.5 + - - +
364F LEU* 3.7 10.6 + - + +
366F SER* 1.3 76.7 - - - +
368F GLU* 1.3 62.2 + - - +
369F LEU 3.1 1.3 - - - -
370F GLU* 2.8 23.5 + - - +
371F LYS* 2.9 15.0 + - - +
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Residues in contact with GLU 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669D ASN* 3.9 21.6 + - - +
364F LEU* 2.9 25.7 + - - +
367F GLU* 1.3 73.1 - - - +
369F LEU* 1.3 56.9 + - - +
371F LYS* 3.3 23.9 + - - +
372F ALA* 2.9 29.4 + - + +
432F LYS* 3.8 37.9 + - + +
433F LEU* 3.6 30.1 - - + -
436F PHE* 5.4 2.0 - - + -
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Residues in contact with LEU 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770C GLU* 3.3 48.5 - - + +
773C LEU* 5.1 8.3 - - + -
774C LEU* 3.7 22.7 - - + +
777C ILE* 5.3 10.1 - - + -
365F LEU* 2.9 36.4 + - + +
366F SER* 4.4 3.6 - - - +
368F GLU* 1.3 78.6 - - - +
370F GLU* 1.3 56.9 + - - +
372F ALA* 3.3 2.9 + - + +
373F LEU* 2.9 31.3 + - - +
390F LEU* 5.5 5.6 - - + -
433F LEU* 3.7 21.3 - - + -
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Residues in contact with GLU 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366F SER 3.6 13.2 + - - +
367F GLU* 2.8 10.6 + - - +
369F LEU* 1.3 79.5 - - - +
371F LYS* 1.3 61.6 + - - +
373F LEU* 3.3 28.5 + - - +
374F SER* 3.2 22.8 + - - +
385F LYS* 4.2 16.9 + - - +
390F LEU* 5.8 3.6 - - - +
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Residues in contact with LYS 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F GLU 2.9 11.9 + - - +
368F GLU* 3.5 27.6 - - - +
370F GLU* 1.3 78.3 - - - +
372F ALA* 1.3 60.2 + - - +
373F LEU 3.1 1.1 + - - -
374F SER* 3.4 17.8 + - - -
375F LYS* 4.2 7.0 - - - -
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Residues in contact with ALA 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F GLU* 2.9 16.8 + - + +
369F LEU* 3.3 4.0 + - + +
371F LYS* 1.3 76.4 - - - +
373F LEU* 1.3 56.4 + - - +
374F SER 3.4 0.2 - - - -
375F LYS* 3.1 42.9 - - + +
423F LEU* 3.2 17.2 - - + +
426F HIS* 6.1 0.9 - - + -
427F GLU* 5.6 1.6 - - - +
433F LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C LEU* 5.2 8.5 - - + -
369F LEU 2.9 16.9 + - - +
370F GLU* 3.5 25.6 - - - +
371F LYS 3.1 0.4 - - - -
372F ALA* 1.3 76.2 - - - +
374F SER* 1.3 57.0 + - - +
375F LYS 3.1 10.6 + - - -
376F LEU* 3.2 33.5 + - + +
381F ALA* 3.7 30.9 - - + +
384F LEU* 4.4 12.3 - - + -
385F LYS* 3.6 38.6 - - + +
390F LEU* 5.9 4.0 - - + -
423F LEU* 4.6 5.8 - - + -
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Residues in contact with SER 374 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F GLU* 3.2 20.4 + - - +
371F LYS* 3.4 10.7 + - - -
372F ALA 3.4 1.4 - - - -
373F LEU* 1.3 75.9 - - - +
375F LYS* 1.3 55.7 + - - +
376F LEU 3.2 10.6 + - - +
381F ALA* 5.7 0.4 - - - -
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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
------------------------------------------------------------
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