Contacts of the helix formed by residues 321 - 333 (chain C) in PDB entry 5T0I
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 ASN 321 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C PRO* 5.3 8.8 - - + +
319C PRO 3.1 8.5 + - - +
320C PRO* 1.3 74.5 - - - +
322C GLU* 1.3 85.7 + - - +
323C GLU* 3.1 21.9 + - + +
324C ALA* 3.0 16.6 + - + +
325C ARG* 2.8 37.6 + - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C ASN* 1.3 92.3 + - - +
323C GLU* 1.3 68.3 + - - +
325C ARG* 3.2 20.0 + - - +
326C LEU* 3.1 36.2 + - + +
348C ALA* 3.6 5.4 - - - +
349C GLU* 3.2 42.6 + - + +
352C PRO* 4.0 18.4 - - - +
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Residues in contact with GLU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLY* 3.3 17.3 - - - +
155C ASP* 5.4 5.6 - - - +
321C ASN* 3.1 25.5 + - + +
322C GLU* 1.3 80.5 - - - +
324C ALA* 1.3 58.4 + - - +
326C LEU* 4.0 11.7 + - + +
327C ASP* 3.0 20.6 + - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLY 4.3 2.0 - - - +
153C GLY* 3.6 19.2 + - - +
154C LEU* 5.7 5.2 - - + -
318C PRO* 6.0 4.0 - - + -
319C PRO 5.3 0.7 - - - +
320C PRO* 4.8 3.8 - - + -
321C ASN* 3.0 28.0 + - + +
323C GLU* 1.3 77.3 - - - +
325C ARG* 1.3 64.0 + - + +
327C ASP* 2.8 17.3 - - - +
328C ILE* 3.1 19.2 - - + +
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C PRO* 2.6 45.6 + - + +
321C ASN* 2.8 40.5 + - - +
322C GLU* 3.2 28.8 + - - +
324C ALA* 1.3 71.0 - - + +
326C LEU* 1.3 66.9 + - - +
328C ILE* 3.9 8.4 - - - +
329C LEU* 3.5 21.7 + - - +
348C ALA* 3.6 33.9 - - + +
351C MET* 3.0 25.2 + - + +
352C PRO* 3.6 2.6 - - - +
353C GLY* 3.0 29.3 + - - +
355C SER 5.5 0.8 + - - -
359C VAL* 4.5 18.9 - - + +
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Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C GLU* 3.1 32.2 + - + +
323C GLU* 4.2 10.3 - - + +
324C ALA 3.2 0.6 - - - -
325C ARG* 1.3 81.2 - - - +
327C ASP* 1.3 62.8 + - + +
329C LEU* 3.8 9.2 + - - +
330C LYS* 4.0 3.6 + - - +
344C LEU* 4.2 18.1 - - + +
345C ARG* 3.6 50.0 - - - +
348C ALA* 3.7 21.8 - - + -
349C GLU* 4.9 8.1 - - + +
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLY* 3.1 8.9 - - - -
153C GLY* 2.4 32.4 + - - -
155C ASP* 5.7 1.7 - - - -
323C GLU 3.0 10.8 - - - +
324C ALA 2.8 12.8 - - - +
326C LEU* 1.3 73.3 - - + +
328C ILE* 1.3 64.7 + - - +
329C LEU 2.9 6.3 + - - -
330C LYS* 3.1 10.2 + - + +
331C ILE* 2.8 35.4 + - + +
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Residues in contact with ILE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C MET 4.0 16.6 - - - +
151C ILE* 4.0 9.6 - - + -
152C GLY 3.5 31.2 - - - +
194C THR* 5.7 4.7 - - - +
195C GLY* 5.9 1.6 - - - -
198C LEU* 4.9 4.0 - - + -
324C ALA* 3.1 22.4 + - + +
325C ARG* 3.9 9.4 - - - -
327C ASP* 1.3 82.2 + - - +
329C LEU* 1.3 61.2 + - - +
331C ILE* 3.5 11.5 - - + +
332C HIS* 2.8 43.8 + - + -
356C GLY 5.7 0.2 - - - +
359C VAL* 3.8 26.2 - - + +
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Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C ARG 3.5 17.0 + - - +
326C LEU 3.9 4.0 - - - +
327C ASP 2.9 0.6 + - - -
328C ILE* 1.3 77.2 - - - +
330C LYS* 1.3 66.9 + - - +
331C ILE 3.0 2.2 + - - -
332C HIS* 3.1 13.8 + - + +
333C SER* 3.1 18.0 + - - +
342C ILE* 5.0 5.4 - - + -
344C LEU* 3.6 29.8 - - + +
347C ILE* 3.8 23.8 - - + -
348C ALA* 5.6 1.6 - - + +
359C VAL* 4.1 20.6 - - + +
362C VAL* 5.3 7.4 - - + -
363C CYS* 3.7 30.5 - - - -
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C LEU 4.0 2.3 + - - +
327C ASP* 3.1 12.3 + - + +
329C LEU* 1.3 79.1 - - - +
331C ILE* 1.3 64.7 + - + +
333C SER* 3.1 17.7 + - - -
334C ARG* 3.2 41.5 + - + +
344C LEU* 3.5 33.8 - - + +
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Residues in contact with ILE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLU* 3.2 26.0 - - - +
150C MET* 3.2 44.1 - - + +
151C ILE 4.2 14.1 - - - +
152C GLY* 4.5 0.9 - - - +
327C ASP* 2.8 25.0 + - + +
328C ILE* 3.5 22.9 - - + +
329C LEU 3.0 0.2 - - - -
330C LYS* 1.3 80.8 - - + +
332C HIS* 1.3 72.4 + - + +
333C SER 3.4 0.2 + - - -
334C ARG* 3.5 36.3 + - - +
335C LYS* 4.7 3.4 + - - +
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Residues in contact with HIS 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C MET 4.9 0.4 + - - -
198C LEU* 4.4 18.5 - - + +
328C ILE* 2.8 45.6 + - + +
329C LEU* 3.1 8.1 + - - +
331C ILE* 1.3 83.4 - - + +
333C SER* 1.3 60.6 + - - +
334C ARG 3.3 0.8 + - - -
335C LYS* 4.2 23.9 + - - +
336C MET* 3.6 19.4 - - + +
359C VAL* 5.0 5.2 - - + +
360C LYS* 3.2 53.2 - - + +
363C CYS* 5.4 10.3 - - + -
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Residues in contact with SER 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C LEU* 3.1 19.6 + - - +
330C LYS* 3.1 14.5 + - - -
332C HIS* 1.3 77.7 - - - +
334C ARG* 1.3 59.5 + - - +
335C LYS 3.4 1.3 - - - -
336C MET* 2.8 36.7 - - - +
338C LEU* 5.3 8.8 + - - +
344C LEU* 5.8 2.6 - - - +
363C CYS* 4.6 12.3 - - - -
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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
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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