Contacts of the helix formed by residues 302 - 308 (chain A) in PDB entry 2ANL
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 GLY 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ASP* 3.3 18.8 - - - +
217A THR* 3.5 5.8 - - - -
219A THR 3.2 21.8 + - - -
220A ILE* 4.7 1.2 - - - +
300A ILE 4.0 0.2 - - - -
301A LEU* 1.3 74.9 - - - +
303A ASP* 1.3 69.2 + - - -
304A PRO* 2.6 9.4 - - - +
305A PHE* 2.9 15.2 + - - +
306A MET* 3.9 5.5 + - - +
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Residues in contact with ASP 303 (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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14A LEU 3.6 8.9 - - - +
15A MET* 3.5 12.8 - - - +
16A PHE* 3.9 14.5 - - + -
158A LEU* 4.3 15.7 - - + +
214A ASP 4.3 0.4 + - - -
215A SER* 3.4 17.8 - - - +
217A THR 2.8 14.4 + - - +
218A SER* 3.2 24.5 - - - -
302A GLY* 1.3 67.3 - - - -
304A PRO* 1.3 61.6 - - + +
306A MET* 2.8 6.0 + - - +
307A ARG* 2.6 53.7 + - + +
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Residues in contact with PRO 304 (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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218A SER 3.9 19.3 - - - +
219A THR 4.3 0.7 - - - +
220A ILE* 3.5 31.2 - - + -
268A LEU* 4.2 3.9 - - + +
272A TYR* 3.5 33.0 - - - +
288A TYR* 4.2 7.9 - - + -
302A GLY* 2.6 8.3 - - - +
303A ASP* 1.3 95.2 - - + +
305A PHE* 1.3 62.1 + - - +
307A ARG* 3.1 37.3 - - - +
308A LYS 3.9 1.9 + - - -
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Residues in contact with PHE 305 (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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197A LEU* 6.4 1.3 - - + -
213A VAL* 5.1 6.1 - - + -
220A ILE* 4.8 0.9 - - + +
259A PHE* 4.5 9.6 - + + -
266A TYR* 4.3 17.3 - + + -
267A THR 5.3 0.4 - - - -
268A LEU* 3.9 22.5 - - + +
301A LEU* 3.7 42.4 - - + +
302A GLY 2.9 10.6 + - - +
304A PRO* 1.3 78.4 - - - +
306A MET* 1.3 56.4 + - + +
308A LYS* 2.5 30.0 + - - +
309A TYR* 2.9 50.4 + + + -
311A THR* 4.5 11.4 - - + -
322A PHE* 3.7 36.8 - + - -
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Residues in contact with MET 306 (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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16A PHE* 5.1 0.2 - - + -
156A PHE* 3.7 30.2 - - + +
158A LEU* 3.1 35.8 + - + +
213A VAL* 4.6 9.2 - - + -
215A SER* 3.5 42.2 - - - +
301A LEU 4.3 9.4 - - - +
302A GLY 4.3 16.6 - - - -
303A ASP* 2.8 9.1 + - - +
305A PHE* 1.3 74.9 - - + +
307A ARG* 1.3 66.2 + - - +
308A LYS 3.1 0.2 - - - -
309A TYR 3.3 21.4 + - - +
310A PHE* 4.4 0.3 + - - -
311A THR* 3.8 26.2 - - + +
313A PHE* 5.0 4.7 - - + -
325A ALA* 5.1 0.7 - - - +
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Residues in contact with ARG 307 (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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14A LEU* 3.4 40.4 + - - +
158A LEU* 3.2 32.3 - - + +
159A PRO 4.0 18.5 - - - +
160A VAL* 5.1 6.5 - - + +
218A SER* 4.4 6.5 + - - -
272A TYR* 4.3 16.9 + - + -
288A TYR* 3.3 35.2 - - - -
303A ASP* 2.6 36.1 + - + +
304A PRO* 3.1 42.5 - - - +
306A MET* 1.3 74.1 - - - +
308A LYS* 1.3 57.0 - - - +
325A ALA* 4.7 3.1 - - - +
327A ASN 4.9 4.7 - - - +
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Residues in contact with LYS 308 (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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267A THR* 2.6 45.4 + - - +
268A LEU* 3.5 16.2 - - + -
269A GLU* 2.9 29.6 + - - -
272A TYR* 3.6 36.6 - - + +
304A PRO 3.9 0.2 + - - -
305A PHE 2.5 14.9 + - - +
307A ARG* 1.3 76.3 - - - +
309A TYR* 1.3 79.7 + - + +
310A PHE 4.0 0.2 - - - -
324A VAL* 3.7 14.8 - - + +
325A ALA* 3.0 24.4 + - - +
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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