Contacts of the helix formed by residues 317 - 336 (chain A) in PDB entry 5UM9
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 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A CYS* 4.1 0.2 - - - -
316A PHE* 1.3 72.2 - - - +
318A GLU* 1.3 64.8 + - - +
319A GLU* 4.5 4.7 - - - -
320A ARG* 3.2 30.9 - - - +
321A ILE* 3.1 23.9 + - - +
7F C 2.9 31.4 + - - -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 4.3 19.6 - - + +
311A CYS* 3.7 15.6 - - + +
316A PHE 3.5 2.6 + - - -
317A SER* 1.3 70.9 - - - +
319A GLU* 1.3 60.6 + - - +
321A ILE* 3.9 0.5 - - - +
322A ARG* 2.6 66.7 + - - +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 3.3 3.5 - - - +
318A GLU* 1.3 75.2 - - - +
320A ARG* 1.3 67.9 + - + +
322A ARG* 3.3 4.7 + - - +
323A SER* 2.9 29.0 + - - +
17D G 5.4 3.8 + - - -
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 5.2 5.9 - - - +
69A TYR* 3.4 28.6 + - + +
317A SER* 3.2 24.2 + - - +
318A GLU 3.5 0.2 - - - -
319A GLU* 1.3 80.0 - - + +
321A ILE* 1.3 57.8 + - + +
323A SER* 2.8 20.5 + - - -
324A GLY* 2.9 14.4 + - - -
14D A 6.0 0.4 - - - -
15D C 3.8 38.7 + - - -
16D G 3.8 37.9 + - - +
4F G 5.0 3.6 - - - +
5F T 5.0 1.8 + - - -
6F C 3.6 47.4 + - - -
7F C 4.5 3.6 - - - +
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Residues in contact with ILE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.0 23.3 - - + -
69A TYR* 4.9 4.0 - - - +
306A LEU* 4.5 14.1 - - + +
307A ILE* 4.6 9.0 - - + -
310A MET* 3.7 36.3 - - + -
311A CYS* 3.9 17.7 - - - -
316A PHE* 3.7 24.0 - - + -
317A SER 3.1 18.7 + - - +
318A GLU 4.0 0.9 - - - +
319A GLU 3.2 0.6 - - - -
320A ARG* 1.3 73.2 - - + +
322A ARG* 1.3 67.8 + - - +
324A GLY* 3.2 0.9 + - - -
325A VAL* 2.9 40.5 + - + +
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU* 3.2 29.6 + - - +
307A ILE* 3.3 36.2 - - + +
318A GLU* 2.6 50.6 + - - +
319A GLU* 3.8 4.5 - - - +
321A ILE* 1.3 78.1 - - - +
323A SER* 1.3 63.0 + - - +
325A VAL* 3.2 7.2 + - - +
326A LYS* 3.0 31.7 + - + +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLU* 2.9 15.7 + - - -
320A ARG* 2.8 24.1 + - - -
322A ARG* 1.3 76.6 - - - +
324A GLY* 1.3 56.2 + - - +
326A LYS* 3.2 10.0 + - - +
327A ARG* 2.9 39.3 + - - +
16D G 4.0 11.5 + - - -
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Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.4 3.6 - - - -
69A TYR* 5.4 2.0 - - - -
72A ILE* 3.5 26.2 - - - +
320A ARG 2.9 16.9 + - - -
321A ILE 3.2 3.1 + - - -
323A SER* 1.3 77.8 + - - +
325A VAL* 1.3 56.0 + - - +
327A ARG* 3.1 19.5 + - - +
328A LEU* 2.9 24.4 + - - +
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.3 9.9 - - + -
301A PRO* 4.3 20.8 - - + +
303A GLU* 3.8 39.7 - - + +
306A LEU* 3.8 27.1 - - + -
307A ILE* 5.8 0.2 - - + -
321A ILE* 2.9 29.1 + - + +
322A ARG* 3.2 4.9 + - - +
324A GLY* 1.3 74.2 - - - +
326A LYS* 1.3 58.3 + - + +
328A LEU* 3.2 8.2 + - + +
329A SER* 2.9 30.3 + - - -
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU* 4.2 23.8 - - - +
322A ARG* 3.0 22.3 + - + +
323A SER* 3.2 10.3 + - - +
325A VAL* 1.3 78.1 - - + +
327A ARG* 1.3 62.0 + - + +
329A SER* 3.0 10.9 + - - +
330A LYS* 3.0 29.6 + - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 4.7 9.7 - - - -
72A ILE* 3.3 26.7 - - + +
73A ARG* 3.5 18.0 - - - +
76A GLU* 2.8 50.3 + - - +
323A SER* 2.9 27.3 + - - +
324A GLY* 3.1 14.9 + - - +
326A LYS* 1.3 76.8 - - + +
328A LEU* 1.3 55.7 + - - +
330A LYS* 3.3 6.2 + - - +
331A SER* 2.9 32.2 + - - -
15D C 4.2 11.4 + - - -
16D G 5.5 9.9 + - - -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 5.6 0.7 - - + -
72A ILE* 4.1 20.3 - - + +
75A MET* 3.6 41.1 - - + -
148A MET* 3.7 51.1 - - + +
150A ILE* 4.8 5.6 - - + -
301A PRO* 4.1 16.2 - - + -
306A LEU* 5.6 2.0 - - + -
324A GLY 2.9 15.6 + - - +
325A VAL* 3.2 7.8 + - - +
327A ARG* 1.3 76.8 - - - +
329A SER* 1.3 56.8 + - - +
331A SER* 2.8 17.9 + - - -
332A ARG* 2.9 16.4 + - + +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 3.4 30.3 - - - +
301A PRO* 4.1 15.9 - - - +
325A VAL* 2.9 15.5 + - - -
326A LYS* 3.0 23.2 + - - +
328A LEU* 1.3 76.3 - - - +
330A LYS* 1.3 57.6 + - - +
332A ARG* 3.8 3.4 - - - +
333A GLN* 2.9 28.4 + - - +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LYS* 3.0 20.8 + - - +
327A ARG* 3.7 5.4 - - - +
329A SER* 1.3 78.5 + - - +
331A SER* 1.3 57.6 + - - +
333A GLN* 3.3 21.0 + - - +
334A GLY* 3.0 22.9 + - - -
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 6.1 0.2 - - - -
75A MET* 3.5 34.7 - - - +
76A GLU* 3.7 18.7 + - - +
327A ARG 2.9 14.7 + - - -
328A LEU* 2.8 23.6 + - - -
330A LYS* 1.3 74.5 - - - +
332A ARG* 1.3 64.4 + - - +
334A GLY* 2.9 12.8 + - - +
335A SER* 2.9 17.4 + - - -
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Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 3.8 19.1 - - + -
298A TRP* 2.9 25.2 + - + +
299A SER* 3.3 23.0 - - - +
300A GLU* 3.2 41.3 + - - +
301A PRO* 4.6 4.5 - - + +
328A LEU* 2.9 18.6 + - + +
329A SER* 3.9 3.8 + - - +
331A SER* 1.3 77.6 + - - +
333A GLN* 1.3 67.8 + - - +
335A SER* 3.7 6.3 - - - -
336A THR* 2.7 65.0 + - + +
337A LEU 5.8 0.6 + - - -
338A GLU* 4.0 28.5 + - - +
406A SM 4.3 4.8 - - - -
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Residues in contact with GLN 333 (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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329A SER 2.9 16.0 + - - +
330A LYS* 3.3 24.5 - - - +
332A ARG* 1.3 84.9 - - - +
334A GLY* 1.3 61.6 + - - +
335A SER 3.5 0.2 + - - -
336A THR* 3.7 12.3 - - - +
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.7 17.1 - - - -
330A LYS 3.0 10.3 + - - -
331A SER* 2.9 10.3 + - - -
333A GLN* 1.3 78.4 - - - +
335A SER* 1.3 56.9 + - - +
336A THR 5.2 0.2 - - - -
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Residues in contact with SER 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.2 19.3 - - - -
28A GLY* 5.4 3.0 - - - -
75A MET* 4.5 8.5 + - - +
78A GLY* 4.3 19.2 - - - -
80A LYS* 2.8 30.3 + - - +
331A SER 2.9 16.2 + - - -
332A ARG* 3.2 4.4 + - - -
334A GLY* 1.3 79.3 - - - +
336A THR* 1.3 72.1 + - - +
337A LEU* 4.4 1.1 + - - +
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Residues in contact with THR 336 (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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75A MET* 5.3 0.4 - - + -
80A LYS* 3.6 24.9 - - + +
298A TRP* 4.2 16.2 - - + -
332A ARG* 2.7 55.3 + - + +
333A GLN* 3.7 14.2 - - - +
334A GLY 3.8 0.4 - - - -
335A SER* 1.3 92.3 - - - +
337A LEU* 1.3 68.8 + - - +
338A GLU* 3.9 4.3 + - - +
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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