Contacts of the helix formed by residues 321 - 334 (chain A) in PDB entry 5UNF
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 VAL 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A MET* 3.5 31.4 - - + +
316A PHE* 2.9 30.4 + - + +
317A LEU* 5.0 5.2 - - - +
320A PHE* 1.4 74.9 - - + +
322A GLY* 1.3 59.6 + - - +
323A ASN 3.2 1.9 + - - -
324A ARG* 3.4 43.5 + - - +
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Residues in contact with GLY 322 (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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142A ARG* 3.4 22.4 + - - -
257A MET* 5.1 1.6 - - - -
316A PHE 4.2 0.6 + - - -
317A LEU 4.4 1.4 + - - -
318A TYR* 3.2 27.1 + - - +
320A PHE 3.3 1.6 - - - -
321A VAL* 1.3 76.6 - - - +
323A ASN* 1.4 60.3 + - - +
324A ARG 3.3 0.4 - - - -
325A PHE* 3.4 19.1 - - - +
326A GLN* 4.0 4.2 + - - +
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Residues in contact with ASN 323 (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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319A CYS 3.8 12.9 + - - +
320A PHE 3.4 14.2 + - - +
321A VAL 3.2 1.2 - - - -
322A GLY* 1.4 76.7 - - - +
324A ARG* 1.4 63.2 + - + +
326A GLN* 3.2 37.7 + - - +
327A GLN* 4.0 4.3 + - - +
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Residues in contact with ARG 324 (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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253A GLN* 4.7 12.4 + - - -
257A MET* 3.4 25.0 - - + +
320A PHE 5.1 3.8 - - - +
321A VAL* 3.4 36.3 + - - +
322A GLY 3.3 0.4 - - - -
323A ASN* 1.4 74.1 - - + +
325A PHE* 1.4 60.6 + - - +
326A GLN 3.1 2.5 - - - -
327A GLN* 3.2 8.7 + - + +
328A LYS* 2.9 42.4 + - + +
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Residues in contact with PHE 325 (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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142A ARG* 4.0 52.9 - - + +
145A SER* 5.6 0.7 - - - -
146A VAL* 4.3 12.3 - - + -
234A ILE* 4.6 7.4 - - + -
254A VAL* 3.6 39.3 - - + +
257A MET* 3.8 34.3 - - + -
258A ALA* 4.7 6.7 - - + -
322A GLY* 3.4 18.7 + - - +
323A ASN 3.3 0.4 - - - -
324A ARG* 1.4 76.9 - - - +
326A GLN* 1.3 55.9 + - - +
328A LYS* 4.6 4.0 - - - +
329A LEU* 3.1 55.1 + - + +
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Residues in contact with GLN 326 (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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77A LYS* 2.9 36.5 + - - +
322A GLY 4.0 4.5 + - - +
323A ASN* 3.2 32.6 + - - +
325A PHE* 1.3 80.0 - - - +
327A GLN* 1.3 62.1 + - - +
329A LEU* 4.1 4.1 - - - +
330A ARG* 3.6 21.1 + - - +
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Residues in contact with GLN 327 (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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323A ASN 4.7 3.6 - - - +
324A ARG* 3.2 11.9 + - + +
326A GLN* 1.3 82.1 + - + +
328A LYS* 1.4 66.3 + - + +
330A ARG* 3.6 8.0 + - - +
331A SER* 2.9 33.1 + - - +
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Residues in contact with LYS 328 (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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246A LYS* 3.7 24.4 - - - +
250A THR* 3.5 37.7 + - + +
253A GLN* 4.9 22.3 - - + +
254A VAL* 3.8 23.2 - - + +
257A MET* 5.6 4.3 - - + -
324A ARG* 2.9 29.2 + - + +
325A PHE* 4.6 1.6 - - - +
327A GLN* 1.4 80.7 - - + +
329A LEU* 1.3 62.2 + - - +
331A SER* 3.9 7.4 + - - +
332A VAL* 3.6 14.4 + - - +
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Residues in contact with LEU 329 (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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145A SER* 3.7 38.4 - - - +
146A VAL* 3.7 35.2 - - + +
238A LEU* 5.2 2.9 - - + -
254A VAL* 4.6 14.8 - - + +
325A PHE* 3.1 32.9 + - + +
326A GLN* 4.1 5.4 - - - +
327A GLN 3.3 0.4 - - - -
328A LYS* 1.3 75.5 - - - +
330A ARG* 1.3 62.1 + - - +
331A SER 3.3 0.4 - - - -
332A VAL* 3.3 28.5 - - + +
333A PHE* 3.3 13.0 + - + +
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Residues in contact with ARG 330 (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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326A GLN 3.6 14.2 + - - +
327A GLN* 3.6 8.3 + - - +
328A LYS 3.5 0.2 - - - -
329A LEU* 1.3 75.5 - - - +
331A SER* 1.4 59.4 + - - +
333A PHE* 4.0 5.3 - - - +
334A ARG* 2.9 28.3 + - - -
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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
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246A LYS* 4.5 12.5 + - - -
247A ASN* 5.1 6.9 - - - +
250A THR* 4.1 14.4 - - - -
327A GLN* 2.9 27.2 + - - +
328A LYS* 3.8 10.5 - - - +
329A LEU 3.3 0.6 - - - -
330A ARG* 1.4 76.8 - - - +
332A VAL* 1.4 63.2 + - - +
333A PHE 3.6 0.2 + - - -
334A ARG* 3.9 12.7 + - - +
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Residues in contact with VAL 332 (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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238A LEU* 4.2 22.0 - - + -
247A ASN* 4.4 18.8 - - + +
250A THR* 3.8 29.2 - - + +
251A ARG* 4.4 11.9 - - + +
254A VAL* 5.6 1.8 - - + -
328A LYS 3.6 8.3 + - - +
329A LEU* 3.3 26.9 - - + +
331A SER* 1.4 76.1 - - - +
333A PHE* 1.4 61.9 + - + +
334A ARG* 5.0 0.9 - - - +
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Residues in contact with PHE 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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149A PRO* 4.5 25.6 - - + -
329A LEU* 3.3 18.4 + - + +
330A ARG* 4.0 5.6 - - - +
331A SER 3.3 0.4 - - - -
332A VAL* 1.4 79.2 - - + +
334A ARG* 1.4 69.7 + - - +
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Residues in contact with ARG 334 (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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330A ARG 2.9 22.7 + - - -
331A SER* 4.0 11.4 - - - +
332A VAL 5.0 0.9 - - - +
333A PHE* 1.4 80.0 - - - +
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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