Contacts of the helix formed by residues 317 - 327 (chain A) in PDB entry 4PE5
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 THR 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A LEU* 3.7 34.3 - - + -
300A ASN 4.4 2.6 + - - +
301A ILE* 3.8 17.4 - - + -
302A THR* 3.1 31.2 + - - +
315A TRP* 3.2 23.2 - - + -
316A LYS* 1.3 75.5 - - - +
318A GLY* 1.3 59.2 + - - +
319A PRO* 3.6 1.1 - - - -
320A LEU* 3.3 12.8 + - + -
321A PHE* 2.9 27.7 + - - +
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Residues in contact with GLY 318 (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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115A ARG* 3.5 24.5 - - - +
117A PRO* 4.3 1.7 - - - +
315A TRP* 2.8 29.8 + - - -
317A THR* 1.3 77.4 - - - +
319A PRO* 1.3 61.0 - - - +
321A PHE* 3.3 2.6 + - - +
322A LYS* 2.9 29.4 + - - +
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Residues in contact with PRO 319 (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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115A ARG* 4.4 17.3 - - + +
314A ILE* 5.1 8.5 - - + -
315A TRP 3.7 8.7 - - - +
316A LYS 3.8 9.2 - - - +
317A THR 3.8 0.9 - - - -
318A GLY* 1.3 89.5 - - - +
320A LEU* 1.3 56.2 + - - +
322A LYS* 3.4 5.0 - - + +
323A ARG* 2.9 25.6 + - - +
207B MET 4.6 7.2 - - - +
208B SER 3.6 22.4 - - - +
209B LEU* 3.7 24.3 - - - +
210B ASP* 4.0 6.3 - - + +
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Residues in contact with LEU 320 (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 LEU* 3.8 21.8 - - + -
298A LYS* 3.4 34.8 - - + +
299A GLU 5.8 0.9 - - - +
301A ILE* 4.4 10.5 - - + -
316A LYS 5.3 0.8 + - - +
317A THR* 3.3 14.5 + - + +
318A GLY 3.2 0.8 - - - -
319A PRO* 1.3 76.3 - - - +
321A PHE* 1.3 67.6 + - - +
322A LYS 3.1 1.3 - - - -
323A ARG* 3.0 40.1 + - - +
324A VAL* 2.9 28.6 + - + +
210B ASP* 3.8 16.7 - - + +
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Residues in contact with PHE 321 (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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88A TYR* 3.0 41.7 - + + -
89A ALA* 4.0 6.3 - - + -
117A PRO* 4.0 9.2 - - + -
288A VAL* 4.4 6.3 - - + -
291A ALA* 3.5 26.2 - - + -
292A VAL* 3.5 27.8 - - + -
295A LEU* 3.8 25.0 - - + +
315A TRP* 3.5 19.3 - + + -
317A THR 2.9 17.4 + - - +
318A GLY 3.6 4.0 - - - +
320A LEU* 1.3 75.7 - - - +
322A LYS* 1.3 57.5 + - - +
324A VAL* 3.1 7.5 + - + +
325A LEU* 2.9 53.8 + - + +
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Residues in contact with LYS 322 (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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117A PRO* 4.4 13.4 - - + +
131A LYS* 6.1 1.2 - - - +
135A LEU 2.9 28.0 + - - -
136A SER* 3.7 27.9 - - - +
137A PHE 4.8 4.0 + - - +
138A LEU* 4.7 10.1 - - + +
318A GLY 2.9 16.8 + - - +
319A PRO* 3.4 7.9 - - + +
321A PHE* 1.3 74.7 - - - +
323A ARG* 1.3 65.9 + - - +
325A LEU* 3.2 7.0 + - - +
326A MET* 2.9 44.0 + - + +
208B SER* 3.3 35.6 + - - -
209B LEU* 3.6 15.2 - - + +
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Residues in contact with ARG 323 (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 LYS* 4.2 8.9 - - - +
319A PRO 2.9 12.1 + - - +
320A LEU* 3.0 26.8 + - - +
322A LYS* 1.3 75.8 - - - +
324A VAL* 1.3 67.0 + - - +
326A MET* 3.4 5.5 + - + +
327A SER* 2.9 36.8 + - - -
209B LEU* 4.4 22.0 - - + -
210B ASP* 2.9 51.6 + - - +
212B GLY* 5.1 6.5 - - - +
213B ASP* 5.2 12.3 + - - +
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Residues in contact with VAL 324 (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 ALA* 3.4 37.9 - - + +
294A GLU* 3.8 29.7 - - + +
295A LEU* 4.5 17.9 - - + -
298A LYS* 5.7 4.0 - - + -
320A LEU* 2.9 25.1 + - + +
321A PHE* 3.1 12.3 + - - +
323A ARG* 1.3 80.5 - - - +
325A LEU* 1.3 59.7 + - - +
327A SER* 3.2 7.7 + - - -
328A SER* 2.8 31.0 + - - +
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Residues in contact with LEU 325 (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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117A PRO* 5.0 4.9 - - + -
119A LEU* 4.1 30.3 - - + -
138A LEU* 3.9 19.1 - - + -
287A VAL* 4.3 5.8 - - + +
288A VAL* 4.1 20.0 - - + +
291A ALA* 3.6 15.7 - - + -
321A PHE* 2.9 67.2 + - + +
322A LYS* 3.2 7.8 + - - +
324A VAL* 1.3 74.2 - - - +
326A MET* 1.3 63.6 + - - +
327A SER 2.9 1.7 + - - -
328A SER* 3.0 20.3 + - - +
340A PHE* 3.5 16.0 - - + -
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Residues in contact with MET 326 (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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137A PHE 5.6 0.4 - - - +
138A LEU* 3.7 17.9 - - + -
322A LYS* 2.9 42.6 + - + +
323A ARG* 3.7 7.2 - - - +
325A LEU* 1.3 75.5 - - - +
327A SER* 1.3 57.8 + - - +
328A SER 4.8 0.7 - - - +
339A GLU* 5.3 1.4 - - - +
340A PHE* 3.6 27.7 + - - +
341A ASN 3.4 14.2 - - - +
342A GLU* 3.2 30.1 - - - +
343A ASP 4.6 0.7 - - - -
344A GLY* 3.6 24.2 - - - +
209B LEU* 4.4 22.0 - - + -
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 4.7 9.5 + - - +
323A ARG* 2.9 29.3 + - - -
324A VAL* 3.4 8.5 + - - -
325A LEU 3.0 0.2 - - - -
326A MET* 1.3 78.0 - - - +
328A SER* 1.3 65.6 + - - +
329A LYS* 3.8 3.6 + - - +
339A GLU* 6.1 0.7 - - - -
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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