Contacts of the helix formed by residues 340 - 359 (chain F) in PDB entry 5D4C
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 340 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011C GLY* 5.4 4.9 - - - -
1013C TYR* 5.2 6.7 - - - -
1064C ASN* 4.1 0.4 - - - -
338F LEU 3.5 4.3 + - - -
339F PRO* 1.3 73.9 - - - +
341F PRO* 1.3 70.1 - - - +
342F VAL* 3.7 10.3 + - - +
343F ASP* 2.8 49.2 + - - -
344F ALA* 3.0 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 341 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010C THR* 4.3 19.1 - - + -
1011C GLY 5.4 0.2 - - - +
1013C TYR* 3.7 31.9 - - + +
1063C ARG* 4.2 17.9 - - + +
1064C ASN* 3.2 27.8 - - - +
1067C TYR* 3.7 28.7 - - + +
339F PRO 4.4 1.1 - - - +
340F SER* 1.3 88.3 - - - +
342F VAL* 1.3 55.4 + - + +
344F ALA* 3.7 1.7 - - - +
345F ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010C THR* 3.8 21.5 - - - +
1067C TYR* 4.0 23.1 - - + +
674D ARG* 3.5 44.1 + - - +
340F SER* 3.1 10.9 - - - +
341F PRO* 1.3 74.1 - - - +
343F ASP* 1.3 63.9 + - - +
345F ALA* 3.4 2.1 + - - +
346F THR* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 343 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339F PRO* 4.3 12.3 - - + +
340F SER* 2.8 34.2 + - - +
342F VAL* 1.3 79.6 - - - +
344F ALA* 1.3 64.2 + - - +
346F THR* 3.1 8.9 + - - +
347F GLN* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064C ASN* 4.1 29.8 - - + +
1068C GLU* 4.0 5.3 - - - +
339F PRO* 4.7 8.4 - - + +
340F SER 3.0 10.7 + - - +
341F PRO 3.7 7.6 - - - +
343F ASP* 1.3 75.2 - - - +
345F ALA* 1.3 63.0 + - - +
347F GLN* 3.5 4.9 + - - +
348F SER* 3.0 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067C TYR* 3.6 23.6 - - + -
1068C GLU* 4.0 17.0 + - + +
1071C ILE* 3.7 18.8 - - + -
674D ARG* 5.4 2.5 - - - +
341F PRO 2.9 18.1 + - - +
342F VAL 3.6 4.7 - - - +
343F ASP 3.2 0.2 - - - -
344F ALA* 1.3 76.0 - - - +
346F THR* 1.3 58.5 + - - +
348F SER* 3.4 0.3 + - - -
349F LEU* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671D LYS* 4.0 28.7 - - + +
674D ARG* 3.9 23.4 + - - +
342F VAL* 2.9 20.5 + - - +
343F ASP* 3.1 8.7 + - - +
345F ALA* 1.3 77.5 - - - +
347F GLN* 1.3 60.0 + - + +
349F LEU* 3.4 7.6 + - - +
350F LEU* 2.9 29.4 + - + +
421F PHE* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 347 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C THR* 4.5 24.7 + - - +
770C GLU* 5.5 6.3 - - - -
771C GLU* 5.5 2.4 + - - +
343F ASP 2.9 15.0 + - - +
344F ALA* 4.1 4.5 - - - +
346F THR* 1.3 80.0 - - + +
348F SER* 1.3 58.7 + - - +
350F LEU* 3.2 15.0 + - + +
351F SER* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068C GLU* 2.7 41.7 + - - -
344F ALA 3.0 14.3 + - - -
345F ALA 3.6 1.8 - - - -
347F GLN* 1.3 76.9 - - - +
349F LEU* 1.3 59.1 + - - +
350F LEU 3.2 0.3 + - - -
351F SER* 3.2 6.6 + - - -
352F GLU* 2.9 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068C GLU* 4.8 1.6 - - + -
1071C ILE* 4.1 26.9 - - + -
1072C LYS* 3.3 31.4 - - + +
669D ASN* 6.2 0.4 - - + +
670D VAL* 4.1 24.7 - - + -
671D LYS* 5.4 4.3 - - + +
674D ARG* 5.7 3.1 - - - +
345F ALA 2.9 22.4 + - - +
346F THR* 3.8 6.5 - - - +
348F SER* 1.3 78.6 - - - +
350F LEU* 1.3 57.4 + - - +
352F GLU* 3.8 9.1 - - - +
353F GLU* 2.9 31.0 + - - +
421F PHE* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C GLU* 3.7 29.8 - - + +
771C GLU* 3.8 24.7 - - - +
774C LEU* 4.1 17.0 - - + -
346F THR* 2.9 17.5 + - + +
347F GLN* 3.3 17.5 - - + +
348F SER 3.1 0.2 - - - -
349F LEU* 1.3 75.1 - - - +
351F SER* 1.3 61.4 + - - +
353F GLU* 3.3 2.0 + - + -
354F LEU* 2.9 43.0 + - + +
418F LEU* 6.0 1.8 - - + -
421F PHE* 3.6 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 351 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C GLU* 3.1 34.7 + - - +
347F GLN* 2.9 17.2 + - - +
348F SER* 3.7 7.6 - - - -
350F LEU* 1.3 76.5 - - - +
352F GLU* 1.3 60.0 + - - +
354F LEU* 3.4 4.2 + - - +
355F GLU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068C GLU* 3.9 2.4 - - - +
1072C LYS* 3.1 40.6 + - - -
348F SER* 2.9 31.1 + - - +
349F LEU* 3.8 13.7 - - - +
351F SER* 1.3 78.6 - - - +
353F GLU* 1.3 56.0 + - - +
355F GLU* 3.4 6.2 + - - +
356F LYS* 2.9 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349F LEU 2.9 19.2 + - - +
350F LEU* 3.9 4.3 - - + +
352F GLU* 1.3 74.3 - - - +
354F LEU* 1.3 60.7 + - - +
356F LYS* 3.3 26.7 + - - +
357F ALA* 2.9 28.1 + - - +
417F LYS* 3.2 36.0 + - - +
418F LEU* 4.0 23.6 - - + +
421F PHE* 4.3 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C GLU* 3.6 50.7 - - + +
773C LEU* 3.7 34.1 - - + -
774C LEU* 4.7 7.0 - - + +
777C ILE* 4.0 7.6 - - + -
350F LEU* 2.9 25.8 + - + +
351F SER* 3.7 4.9 - - - +
353F GLU* 1.3 75.2 - - - +
355F GLU* 1.3 59.5 + - - +
357F ALA* 3.3 4.9 + - + +
358F LEU* 2.9 34.5 + - + +
375F LEU* 4.9 7.9 - - + -
418F LEU* 3.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 355 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351F SER 2.9 17.4 + - - +
352F GLU* 3.7 6.7 - - - +
354F LEU* 1.3 75.0 - - - +
356F LYS* 1.3 65.0 + - + +
358F LEU* 4.3 3.4 - - - +
359F SER* 3.0 34.7 + - - -
370F LYS* 2.7 38.1 + - - -
375F LEU* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 356 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352F GLU* 2.9 27.9 + - - +
353F GLU* 3.5 34.3 - - - +
355F GLU* 1.3 75.8 - - - +
357F ALA* 1.3 59.1 + - - +
359F SER* 2.8 21.5 + - - -
360F LYS* 4.0 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777C ILE* 5.6 0.7 - - + -
353F GLU* 2.9 17.3 + - - +
354F LEU* 3.7 6.5 - - + +
355F GLU 3.1 0.4 - - - -
356F LYS* 1.3 78.9 - - - +
358F LEU* 1.3 61.1 + - + +
359F SER 3.6 0.2 + - - -
360F LYS* 3.6 17.2 + - - +
361F LEU* 4.4 1.0 - - - +
408F LEU* 3.2 30.1 - - + +
411F HIS* 5.0 2.3 - - + -
418F LEU* 4.1 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773C LEU* 3.7 25.8 - - + -
354F LEU* 2.9 20.7 + - + +
355F GLU* 3.2 8.0 + - - +
357F ALA* 1.3 74.3 - - + +
359F SER* 1.3 62.5 + - - +
360F LYS 3.2 2.0 - - - -
361F LEU* 3.5 23.6 + - + +
366F ALA* 3.5 27.3 - - + +
369F LEU* 4.0 16.4 - - + -
370F LYS* 3.6 39.9 - - + -
375F LEU* 4.4 5.6 - - + -
408F LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355F GLU* 3.0 20.4 + - - -
356F LYS* 2.8 24.8 + - - -
358F LEU* 1.3 74.5 - - - +
360F LYS* 1.3 67.2 + - - +
361F LEU 3.1 14.4 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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