Contacts of the strand formed by residues 316 - 322 (chain D) in PDB entry 4N38
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D SER* 3.6 11.4 - - - +
211D LEU* 3.5 37.2 - - + +
212D ILE 3.6 10.3 - - - +
213D PRO* 3.7 8.7 - - + +
249D LEU* 4.2 19.7 - - + -
250D ILE 3.6 10.1 + - - +
251D TYR* 3.1 40.5 - - + +
252D TRP* 2.7 28.6 + - - +
315D PHE* 1.3 80.6 - - - +
317D PHE* 1.3 54.2 + - - +
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Residues in contact with PHE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D TYR* 3.5 1.8 - + - +
210D SER* 2.9 45.5 + - - -
212D ILE* 3.2 23.8 - - + -
214D LYS* 3.8 22.4 - - + -
219D ALA* 3.5 31.2 - - + -
222D PHE* 3.3 45.1 - + + -
223D CYS* 4.0 4.7 - - - -
230D LEU* 3.9 2.7 - - + -
251D TYR* 3.5 2.9 - - - -
252D TRP* 3.5 16.8 - - + +
315D PHE 4.1 4.9 - - - -
316D LEU* 1.3 80.0 - - - +
318D ILE* 1.3 64.0 + - - +
319D CYS* 3.8 19.3 - - - -
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Residues in contact with ILE 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D TYR* 4.2 11.9 - - + -
208D TYR 3.2 7.2 - - - +
209D PHE* 3.4 42.0 - - + -
230D LEU* 3.3 9.1 - - - +
231D THR* 3.0 42.9 + - + +
242D LEU* 4.2 9.0 - - + +
246D ALA* 5.3 0.2 - - + -
251D TYR* 3.6 25.4 - - + -
252D TRP 3.0 8.5 + - - +
253D ILE* 4.3 4.7 - - + -
298D ILE* 4.2 23.1 - - + -
317D PHE* 1.3 77.8 - - - +
319D CYS* 1.3 72.9 + - - +
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Residues in contact with CYS 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D TRP* 3.8 13.5 - - + -
207D TYR* 3.2 5.9 - - - +
208D TYR* 2.9 38.5 + - + -
222D PHE* 4.3 4.9 - - - -
223D CYS* 2.0 49.8 - - - -
226D ARG* 5.9 0.7 - - - -
228D SER* 3.3 13.7 - - - +
229D HIS 3.3 4.9 - - - -
317D PHE* 3.8 17.9 - - - -
318D ILE* 1.3 79.0 - - - +
320D LYS* 1.3 61.9 + - - +
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Residues in contact with LYS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D ASN* 3.6 31.2 - - + +
206D PHE 3.3 4.3 - - - -
207D TYR* 3.5 17.5 - - + -
228D SER* 3.3 2.9 - - - -
229D HIS* 2.7 32.4 + - + +
230D LEU 5.0 0.2 - - - +
231D THR* 3.4 30.7 - - - +
232D SER* 3.2 27.6 + - - +
234D THR* 5.0 3.8 + - - +
238D GLU* 2.7 31.9 + - - +
268D ASP* 4.8 4.5 + - - +
319D CYS* 1.3 77.2 - - - +
321D ARG* 1.3 63.2 + - - +
322D PRO* 4.7 1.1 - - + +
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Residues in contact with ARG 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D TRP* 3.3 62.1 - - + +
205D ASN* 3.4 6.3 - - - -
206D PHE* 2.8 68.9 + - + +
226D ARG 4.1 9.8 + - - -
227D ASN* 3.5 33.9 - - - +
228D SER* 3.6 3.6 - - - -
320D LYS* 1.3 76.2 - - - +
322D PRO* 1.3 80.1 + - + +
324D VAL* 5.3 7.8 - - - +
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Residues in contact with PRO 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A PRO* 5.6 9.4 - - + -
272A PHE 4.9 13.9 - - - +
273A ASN* 5.8 4.0 - - - -
274A LYS 6.1 0.9 - - - +
204D GLY 3.9 2.2 - - - +
205D ASN* 3.2 15.5 - - - +
206D PHE* 4.8 0.4 - - - -
227D ASN 5.1 2.5 - - - +
320D LYS 4.7 0.9 - - - +
321D ARG* 1.3 101.2 + - + +
323D TYR* 1.3 69.2 + - - +
324D VAL* 3.4 20.4 + - + +
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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