Contacts of the helix formed by residues 316 - 331 (chain C) in PDB entry 3OP5
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 LEU 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305C THR* 5.8 0.2 - - - +
309C LEU* 5.1 1.6 - - - +
314C LYS 3.7 4.4 + - - +
315C PRO* 1.3 71.3 - - - +
317C TYR* 1.4 63.4 + - - +
318C GLU* 3.3 4.0 - - + -
319C ASN* 3.1 33.3 + - + +
320C LEU* 3.3 15.4 + - - +
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Residues in contact with TYR 317 (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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162C LEU* 4.5 10.6 - - + +
165C LEU 4.6 0.4 - - - -
166C GLU* 3.6 62.8 - - + +
169C HIS* 2.7 44.6 + + - +
170C GLU* 4.6 11.4 - - - -
240C ARG* 3.5 2.4 + - - -
244C LEU* 4.7 9.9 - - + -
314C LYS* 4.6 7.9 - - + -
315C PRO* 3.2 54.1 + - + +
316C LEU* 1.4 68.6 - - - +
318C GLU* 1.3 59.2 + - - +
320C LEU* 3.3 14.9 + - + +
321C ARG* 3.0 37.4 + - - +
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLU* 4.6 3.8 - - - +
316C LEU* 3.3 1.9 - - + -
317C TYR* 1.3 78.7 - - - +
319C ASN* 1.3 58.6 + - - +
321C ARG* 2.9 40.3 + - - +
322C ASP* 3.0 40.4 + - - +
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Residues in contact with ASN 319 (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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305C THR* 3.5 29.9 + - - +
316C LEU* 3.1 30.9 + - + +
318C GLU* 1.3 75.4 - - - +
320C LEU* 1.4 62.3 + - - +
322C ASP* 3.4 12.9 + - - +
323C ILE* 3.2 31.4 + - - +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LEU* 3.9 17.7 - - + -
244C LEU* 3.7 37.9 - - + -
302C TYR* 3.7 27.1 - - + -
305C THR* 3.9 32.8 - - + -
306C VAL* 4.2 8.3 - - + -
309C LEU* 5.7 1.1 - - + -
315C PRO* 4.6 5.8 - - + -
316C LEU 3.3 13.2 + - - +
317C TYR* 3.3 15.2 + - + +
319C ASN* 1.4 74.0 - - - +
321C ARG* 1.3 64.1 + - - +
323C ILE* 3.4 12.1 + - + +
324C LEU* 3.3 25.6 + - - +
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Residues in contact with ARG 321 (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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159C LEU* 3.8 24.5 + - + +
160C ARG* 6.2 0.7 - - - +
162C LEU* 3.5 35.4 + - + +
163C ASP* 3.1 31.0 + - - +
166C GLU* 2.6 28.9 + - - +
317C TYR* 3.0 24.9 + - - +
318C GLU* 2.9 49.3 + - - +
320C LEU* 1.3 74.3 - - - +
322C ASP* 1.4 53.0 + - - +
324C LEU* 3.2 4.5 + - - +
325C LEU* 2.8 46.0 + - + +
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Residues in contact with ASP 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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318C GLU* 3.0 27.8 + - - +
319C ASN* 3.6 12.9 - - - +
320C LEU 3.4 0.2 - - - -
321C ARG* 1.4 72.0 - - - +
323C ILE* 1.4 59.9 + - + +
325C LEU* 3.3 18.1 + - - +
326C GLN* 2.9 30.7 + - - +
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Residues in contact with ILE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C GLU* 3.3 36.8 - - + +
301C LYS* 3.8 25.7 - - + +
302C TYR* 3.8 14.6 - - + +
305C THR* 3.4 31.0 - - - +
319C ASN* 3.2 27.3 + - - +
320C LEU* 3.5 15.0 - - - +
321C ARG 3.3 0.2 - - - -
322C ASP* 1.4 76.3 - - + +
324C LEU* 1.3 62.5 + - + +
326C GLN* 3.3 13.5 + - - +
327C GLY 3.4 8.3 + - - -
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C LEU* 3.6 31.1 - - + +
158C SER* 3.6 30.5 - - - -
159C LEU* 3.9 17.0 - - + +
162C LEU* 3.7 27.8 - - + -
251C MET* 4.2 20.4 - - + -
298C GLU* 4.6 7.9 - - + -
299C ILE* 5.2 1.1 - - + -
302C TYR* 4.4 17.5 - - + -
320C LEU 3.3 8.9 + - - +
321C ARG 3.2 6.5 + - - +
323C ILE* 1.3 76.2 - - + +
325C LEU* 1.4 64.3 + - - +
327C GLY* 3.2 11.1 + - - -
328C LEU* 3.2 14.3 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 4.0 15.5 - - + -
321C ARG* 2.8 31.8 + - + +
322C ASP* 3.7 18.8 - - - +
324C LEU* 1.4 72.5 - - - +
326C GLN* 1.4 59.4 + - - +
328C LEU* 3.3 11.3 + - + +
329C LYS* 3.1 26.0 + - - +
335C ASP* 3.7 33.7 - - + +
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C GLU* 5.8 0.7 - - + -
301C LYS* 6.4 1.3 - - + -
322C ASP 2.9 16.8 + - - +
323C ILE* 3.5 8.5 - - - +
324C LEU 3.3 0.2 - - - -
325C LEU* 1.4 74.1 - - - +
327C GLY* 1.3 58.0 + - - +
329C LYS* 3.4 10.2 + - - +
330C ALA* 3.0 27.9 + - - +
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Residues in contact with GLY 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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151C ARG* 4.2 1.0 + - - -
155C LEU* 3.7 8.5 - - - +
298C GLU* 3.6 32.0 - - - +
323C ILE 3.4 4.6 + - - -
324C LEU 3.2 9.6 + - - -
326C GLN* 1.3 76.3 - - - +
328C LEU* 1.4 60.8 + - - +
330C ALA* 3.4 8.4 - - - +
331C ILE* 3.3 25.8 + - - +
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Residues in contact with LEU 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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152C LYS* 3.8 26.2 - - + +
155C LEU* 3.9 27.6 - - + -
156C GLN* 3.4 28.0 - - - +
159C LEU* 3.7 26.0 - - + -
324C LEU 3.2 11.0 + - - +
325C LEU* 3.3 12.8 + - + +
327C GLY* 1.4 73.4 - - - +
329C LYS* 1.4 57.4 + - - +
331C ILE* 3.2 16.7 - - + +
333C SER* 2.8 33.3 + - - +
334C LYS* 4.3 10.8 - - - +
335C ASP* 4.0 13.7 - - + +
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Residues in contact with LYS 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 LEU 3.1 13.5 + - - +
326C GLN* 3.6 12.8 - - - +
328C LEU* 1.4 74.3 - - - +
330C ALA* 1.3 62.2 + - - +
332C GLY* 3.1 14.2 + - - -
333C SER 3.8 10.5 + - - +
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Residues in contact with ALA 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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151C ARG* 4.1 16.2 - - - +
326C GLN 3.0 14.0 + - - +
327C GLY* 3.4 13.2 - - - +
328C LEU 3.3 0.4 - - - -
329C LYS* 1.3 76.1 - - - +
331C ILE* 1.4 57.5 + - - +
332C GLY 3.3 2.1 + - - -
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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
----------------------------------------------------------
151C ARG* 3.7 46.4 - - + +
152C LYS* 3.8 38.8 - - + +
155C LEU* 4.8 1.6 - - + -
327C GLY 3.3 7.6 + - - +
328C LEU* 3.2 20.6 - - + +
329C LYS 3.3 0.2 - - - -
330C ALA* 1.4 73.5 - - - +
332C GLY* 1.3 57.7 + - - +
333C SER* 3.5 16.1 + - - -
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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