Contacts of the helix formed by residues 293 - 305 (chain A) in PDB entry 3LD8
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLU* 4.7 0.8 + - - -
67A TYR* 3.3 22.7 - - + +
192A GLY 3.9 12.0 + - - +
194A SER* 2.9 32.3 + - - +
288A PHE* 3.4 17.0 + - - -
289A ALA* 3.3 6.8 - - - -
290A SER* 2.8 31.3 + - - +
292A THR* 1.3 75.7 - - - +
294A PHE* 1.3 62.7 + - - +
295A PRO* 3.2 3.8 - - - -
296A VAL* 2.9 7.9 + - + +
297A VAL* 2.7 36.1 + - - +
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Residues in contact with PHE 294 (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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160A LEU* 3.7 22.4 - - + -
289A ALA* 5.3 0.4 - - + -
290A SER 3.0 18.4 + - - +
291A SER* 4.0 5.4 - - - +
292A THR 3.5 0.2 - - - -
293A ASN* 1.3 78.8 + - - +
295A PRO* 1.3 67.0 - - + +
297A VAL* 4.1 4.7 - - + -
298A TRP* 2.7 61.0 + + + +
312A TRP* 3.7 26.7 - + - -
316A LEU* 3.7 32.1 - - + -
323A LEU* 3.8 43.7 - - + -
326A LEU* 4.5 10.8 - - + -
327A ALA* 4.7 3.8 - - + -
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Residues in contact with PRO 295 (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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291A SER 3.9 10.3 - - - +
292A THR 3.9 7.2 - - - +
293A ASN 3.4 4.5 - - - -
294A PHE* 1.3 98.2 - - + +
296A VAL* 1.3 59.9 + - + +
298A TRP* 3.8 4.6 - - + +
299A HIS* 3.0 29.8 + - - +
326A LEU* 4.6 25.4 - - + -
330A VAL* 5.5 9.7 - - + +
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Residues in contact with VAL 296 (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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67A TYR* 4.5 15.3 - - + +
192A GLY* 4.3 13.9 - - - +
292A THR 6.0 0.2 - - - +
293A ASN* 2.9 8.3 + - - +
295A PRO* 1.3 75.7 - - + +
297A VAL* 1.3 67.0 + - - +
299A HIS* 3.3 9.1 + - + +
300A LYS* 2.9 48.0 + - + +
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Residues in contact with VAL 297 (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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161A PHE* 3.9 20.0 - - + -
191A LEU 3.3 22.3 - - - +
192A GLY 3.6 15.0 - - - +
193A THR* 4.0 8.1 - - + -
289A ALA* 4.0 6.3 - - + -
293A ASN* 2.7 40.7 + - - +
294A PHE* 3.7 7.2 - - - +
296A VAL* 1.3 72.6 - - - +
298A TRP* 1.3 52.9 + - - +
300A LYS* 3.7 1.7 - - - +
301A THR* 2.7 38.9 + - - +
312A TRP* 3.6 26.9 - - + -
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Residues in contact with TRP 298 (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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294A PHE* 2.7 45.0 + + + +
295A PRO* 3.8 3.4 - - + +
297A VAL* 1.3 71.1 - - - +
299A HIS* 1.3 73.1 + - - +
301A THR* 3.0 13.9 + - - +
302A VAL* 3.0 35.8 + - + +
309A SER* 3.4 34.3 - - - -
310A ARG* 5.3 0.4 - - + -
312A TRP* 3.8 27.8 - + - -
313A TYR* 3.7 27.6 - + + -
316A LEU* 5.3 1.1 - - + -
327A ALA* 3.6 23.3 - - + +
330A VAL* 3.9 23.1 - - + -
331A ASP* 3.1 27.5 + - - -
352A SO4 4.3 9.4 - - - -
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Residues in contact with HIS 299 (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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295A PRO 3.0 16.0 + - - +
296A VAL* 3.6 8.5 - - + +
298A TRP* 1.3 84.2 - - + +
300A LYS* 1.3 71.3 + - + +
302A VAL* 3.1 26.3 - - + +
303A ARG* 3.5 49.7 + - + +
330A VAL* 5.2 14.8 - - + +
334A GLU* 5.5 6.8 + - - -
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Residues in contact with LYS 300 (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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188A ILE* 6.5 1.1 - - - -
189A ASP 5.9 0.4 - - - -
191A LEU* 3.3 13.7 - - - +
192A GLY* 3.2 32.8 - - - +
296A VAL* 2.9 28.0 + - + +
297A VAL 3.7 3.1 - - - +
299A HIS* 1.3 86.4 - - + +
301A THR* 1.3 66.1 + - - +
303A ARG* 3.2 10.8 + - - +
304A GLY* 2.9 22.9 + - - -
348A SO4 3.0 43.6 + - - +
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Residues in contact with THR 301 (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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161A PHE* 3.4 21.7 - - - -
191A LEU* 3.7 16.1 - - + +
297A VAL* 2.7 23.6 + - - +
298A TRP* 3.0 4.0 + - - -
300A LYS* 1.3 73.3 - - - +
302A VAL* 1.3 56.8 + - - +
305A ARG* 2.7 30.2 + - + +
308A LEU* 3.9 20.6 - - + -
309A SER* 3.5 30.7 - - - +
312A TRP* 4.0 14.5 - - + -
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Residues in contact with VAL 302 (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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298A TRP* 3.0 47.2 + - + +
299A HIS* 3.1 22.7 - - + +
301A THR* 1.3 75.9 - - - +
303A ARG* 1.3 79.9 + - + +
306A PRO* 3.1 25.1 - - - +
309A SER* 3.7 20.9 - - - +
331A ASP* 4.7 8.5 - - - +
352A SO4 5.5 2.0 - - - +
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Residues in contact with ARG 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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299A HIS* 3.6 43.3 + - + +
300A LYS* 3.2 13.4 + - - +
302A VAL* 1.3 88.5 - - + +
304A GLY* 1.3 59.4 + - - +
306A PRO* 4.0 6.9 - - - +
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Residues in contact with GLY 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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191A LEU* 5.3 4.0 - - - -
300A LYS 2.9 13.4 + - - -
303A ARG* 1.3 78.4 - - - +
305A ARG* 1.3 69.1 + - - +
306A PRO* 3.4 6.6 - - - +
348A SO4 5.6 3.1 - - - -
351A SO4 3.8 2.9 + - - -
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Residues in contact with ARG 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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168A ARG 4.2 12.1 + - - -
170A PRO* 3.9 18.7 - - - +
171A PRO* 6.0 0.2 - - - +
191A LEU* 4.9 16.6 - - + -
301A THR* 2.7 22.9 + - + +
304A GLY* 1.3 82.7 - - - +
306A PRO* 1.3 64.8 - - - +
308A LEU* 3.1 37.2 - - + +
309A SER 3.0 17.8 + - - -
351A SO4 2.8 37.3 + - - +
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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