Contacts of the helix formed by residues 316 - 331 (chain C) in PDB entry 4AD7
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 316 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C SER 3.3 21.0 + - - -
313C VAL* 2.7 13.2 + - - -
315C GLY* 1.3 79.3 - - - +
317C VAL* 1.3 62.8 + - - +
318C HIS* 3.2 7.2 - - - -
319C THR* 3.0 30.8 + - - +
320C TRP* 3.6 15.5 + - - -
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.2 15.7 - - + -
118C SER* 3.3 3.7 + - - +
144C LEU* 5.2 1.8 - - + -
145C TYR* 3.6 18.8 - - + +
148C LEU* 4.2 26.0 - - + -
209C LEU* 3.9 21.5 - - + -
217C PHE* 5.0 2.9 - - + -
313C VAL* 3.0 23.3 + - + +
314C ILE* 4.3 2.5 - - - +
316C SER* 1.3 76.1 - - - +
318C HIS* 1.3 58.0 + - - +
320C TRP* 2.9 29.2 + - - +
321C LEU* 3.0 27.6 + - + +
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Residues in contact with HIS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C SER* 2.8 39.9 + - - +
121C THR* 3.4 33.7 - - + +
122C LEU* 3.9 21.5 - - + -
125C THR* 6.4 0.9 - - - -
126C PHE* 3.6 6.8 - + + -
145C TYR* 3.6 3.8 + - - +
315C GLY 3.3 20.4 - - - -
316C SER* 4.5 3.8 - - - -
317C VAL* 1.3 77.9 - - - +
319C THR* 1.3 79.9 + - - +
321C LEU* 3.7 9.2 - - - -
322C ALA* 2.9 31.7 + - - +
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Residues in contact with THR 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C SER* 3.0 25.6 + - - +
318C HIS* 1.3 93.1 + - - +
320C TRP* 1.3 77.2 + - + +
322C ALA* 3.8 5.2 - - - +
323C GLU* 2.9 32.6 + - + +
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Residues in contact with TRP 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TRP* 5.1 0.2 - - - -
205C ALA* 3.4 12.7 - - + +
208C GLU* 4.4 29.2 - - + -
209C LEU* 4.0 34.8 - - + -
212C ARG* 3.5 38.4 - - - -
313C VAL* 3.6 23.7 - - + +
316C SER* 3.6 26.4 + - - -
317C VAL* 2.9 13.1 + - - +
319C THR* 1.3 85.7 - - + +
321C LEU* 1.3 62.1 + - - +
323C GLU* 3.5 29.7 + - - -
324C ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 3.6 22.4 - - + -
126C PHE* 3.9 13.7 - - + -
141C PHE* 3.7 20.4 - - + -
144C LEU* 4.1 24.9 - - + -
145C TYR* 4.2 8.5 - - + +
166C PHE* 4.5 4.5 - - + -
167C TRP* 3.8 24.7 - - + -
209C LEU* 4.1 12.6 - - + -
317C VAL* 3.0 32.2 + - + +
318C HIS 3.9 3.8 - - - +
319C THR 3.3 0.2 - - - -
320C TRP* 1.3 75.9 - - - +
322C ALA* 1.3 61.1 + - - +
324C ALA* 3.1 5.5 + - - +
325C ILE* 2.9 31.7 + - - +
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Residues in contact with ALA 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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125C THR* 6.3 1.6 - - + -
126C PHE* 3.4 18.5 - - + -
130C PHE* 3.4 21.6 - - + -
318C HIS 2.9 18.4 + - - +
319C THR* 3.8 5.2 - - - +
321C LEU* 1.3 75.4 - - - +
323C GLU* 1.3 59.0 + - - +
325C ILE 3.3 0.5 + - - -
326C ASN* 2.9 31.9 + - - +
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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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202C PHE 4.0 1.9 - - - +
204C GLU* 4.5 11.5 + - - +
205C ALA* 4.1 18.7 + - + +
208C GLU* 5.6 1.4 - - - +
319C THR* 2.9 23.3 + - - +
320C TRP* 3.8 33.3 - - - +
322C ALA* 1.3 75.8 - - - +
324C ALA* 1.3 57.5 + - - +
326C ASN* 2.5 33.1 + - - +
327C ALA* 3.5 6.9 + - - +
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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
----------------------------------------------------------
167C TRP* 3.5 36.1 - - + -
202C PHE* 3.4 24.4 - - + +
205C ALA* 3.6 12.6 - - + -
320C TRP 2.9 15.1 + - - +
321C LEU* 3.1 10.3 + - + +
323C GLU* 1.3 76.0 - - - +
325C ILE* 1.3 65.8 + - + +
327C ALA* 3.3 15.2 + - - +
328C LEU 3.6 2.1 + - - -
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Residues in contact with ILE 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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126C PHE* 3.5 33.2 - - + -
130C PHE* 3.6 40.2 - - + -
133C LEU* 4.5 12.1 - - + +
134C TYR* 5.4 4.5 - - + +
141C PHE* 3.6 26.2 - - + -
170C LEU* 5.6 5.6 - - + -
174C LEU* 5.9 9.0 - - + -
202C PHE* 5.1 7.2 - - + -
321C LEU 2.9 12.0 + - - +
324C ALA* 1.3 72.9 - - + +
326C ASN* 1.3 66.9 + - - +
327C ALA 3.0 1.8 - - - -
328C LEU* 3.0 10.5 + - + +
329C GLN* 2.9 28.6 + - + +
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Residues in contact with ASN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 4.4 10.9 - - + -
322C ALA 2.9 16.0 + - - +
323C GLU* 2.5 41.7 + - - +
325C ILE* 1.3 76.6 - - - +
327C ALA* 1.3 62.7 + - - +
329C GLN* 3.8 7.8 - - - +
330C ASP* 2.9 53.1 + - - +
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PRO 3.2 18.6 - - - +
202C PHE 3.4 24.5 - - - +
203C GLY* 3.8 5.6 - - - +
323C GLU 3.8 5.4 - - - +
324C ALA 3.3 5.8 + - - +
325C ILE 3.0 0.6 - - - -
326C ASN* 1.3 86.0 - - - +
328C LEU* 1.3 56.7 + - - +
330C ASP* 3.6 3.5 + - - +
331C ASN* 2.9 38.7 + - - +
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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
----------------------------------------------------------
133C LEU* 6.0 1.3 - - + -
171C LEU* 3.7 19.1 - - + -
174C LEU* 3.8 31.4 - - + -
175C PHE* 6.4 1.1 - - + -
178C LEU* 5.1 8.4 - - + +
201C PRO* 3.7 28.5 - - + +
202C PHE* 3.6 38.8 - - + -
324C ALA 3.6 3.8 + - - +
325C ILE* 3.0 10.8 + - + +
327C ALA* 1.3 78.3 - - - +
329C GLN* 1.3 61.1 + - + +
331C ASN* 3.5 5.0 - - + +
332C ARG* 2.9 27.2 + - - +
335C LEU* 5.0 15.0 - - + -
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Residues in contact with GLN 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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129C ALA 5.1 1.7 - - - +
130C PHE* 4.2 23.2 + - - -
133C LEU* 3.3 35.8 - - + +
325C ILE* 2.9 21.3 + - + +
326C ASN* 3.4 8.9 + - - +
328C LEU* 1.3 76.7 - - - +
330C ASP* 1.3 66.7 + - - +
332C ARG* 3.3 28.1 - - - +
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Residues in contact with ASP 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 ASN* 2.9 38.3 + - - +
327C ALA* 4.0 2.6 - - - +
329C GLN* 1.3 78.6 - - - +
331C ASN* 1.3 70.2 + - - +
332C ARG 3.2 1.4 + - - -
333C ASP* 4.2 9.2 + - - +
334C THR* 4.8 2.3 + - - -
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Residues in contact with ASN 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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200C ARG 4.2 6.1 + - - -
201C PRO* 3.9 23.4 + - + +
327C ALA* 2.9 21.9 + - - +
328C LEU* 3.5 9.2 - - + +
330C ASP* 1.3 83.8 - - - +
332C ARG* 1.3 63.2 + - - +
333C ASP 3.1 3.4 - - - +
334C THR* 2.7 43.1 + - - +
335C LEU* 3.8 8.5 - - + +
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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
------------------------------------------------------------
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