Contacts of the strand formed by residues 324 - 337 (chain D) in PDB entry 3RN5
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 324 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D ILE* 3.8 11.7 - - + -
255D LEU* 3.5 39.3 - - + -
256D GLN* 4.4 12.1 - - + +
290D LYS 3.2 23.5 + - - +
291D MET* 3.6 18.6 - - + -
292D GLU* 3.4 21.8 + - - +
317D LEU* 4.0 16.2 - - + -
319D LYS* 3.1 18.1 + - - +
320D ASN* 3.7 6.3 - - - +
321D GLY 3.5 17.4 + - - +
323D LYS* 1.3 79.9 - - - +
325D GLN* 1.3 64.0 + - - +
326D LEU* 4.6 0.2 - - + -
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Residues in contact with GLN 325 (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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281D LEU* 5.6 2.2 - - - +
291D MET* 4.9 0.2 - - - -
292D GLU* 3.1 27.5 + - + +
293D VAL 5.3 0.4 - - - -
294D LEU* 4.6 15.2 - - - +
317D LEU* 3.4 4.9 - - - +
318D SER* 3.3 15.9 + - - -
319D LYS* 2.8 71.5 + - + +
324D LEU* 1.3 76.0 - - - +
326D LEU* 1.3 75.3 + - - +
327D THR* 3.3 21.0 - - - +
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D LEU* 4.6 0.9 - - + -
264D VAL* 3.8 32.1 - - + -
291D MET* 3.4 33.2 - - - -
292D GLU 3.1 3.0 + - - +
293D VAL* 3.5 41.5 - - + -
294D LEU 3.8 1.4 + - - -
312D LEU* 3.8 13.7 - - + -
315D PHE* 4.6 6.7 - - + -
316D THR 3.1 13.5 - - - +
317D LEU* 3.3 29.2 - - + -
318D SER* 3.9 0.2 - - - -
324D LEU* 4.6 2.7 - - + -
325D GLN* 1.3 89.7 + - - +
327D THR* 1.3 66.7 + - - +
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Residues in contact with THR 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D LEU* 5.0 7.4 - - + -
315D PHE* 3.9 5.2 - - - -
316D THR* 2.8 40.6 + - - -
318D SER* 3.1 33.9 - - - +
325D GLN* 3.3 17.3 - - - +
326D LEU* 1.3 77.6 - - - +
328D SER* 1.3 62.9 + - - +
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Residues in contact with SER 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ASN* 4.7 3.5 + - - -
294D LEU 3.2 17.9 + - - -
295D GLY* 4.5 0.2 - - - -
296D VAL* 4.3 19.0 - - - +
315D PHE* 3.2 29.2 - - - -
327D THR* 1.3 73.7 - - - +
329D GLY* 1.3 61.8 + - - +
332D SER* 3.2 15.0 - - - -
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Residues in contact with GLY 329 (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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3D EDO 3.3 19.6 + - - -
327D THR 3.8 2.0 + - - -
328D SER* 1.3 76.9 - - - +
330D VAL* 1.3 66.5 + - - -
331D HIS 3.1 3.8 - - - -
332D SER* 2.6 24.3 + - - +
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Residues in contact with VAL 330 (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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3D EDO 4.3 2.2 + - - -
165D PHE* 4.4 2.3 - - - -
167D PHE* 3.2 50.9 - - + +
168D GLU 4.3 9.0 - - - +
169D THR* 4.3 7.4 - - + -
329D GLY* 1.3 72.1 - - - +
331D HIS* 1.3 72.5 + - + +
332D SER 3.6 4.3 + - - +
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Residues in contact with HIS 331 (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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3D EDO 4.1 7.5 + - - +
165D PHE* 3.6 7.8 - - - -
167D PHE* 3.6 26.2 - + - -
176D MET* 2.7 27.6 - - - -
178D HIS* 2.7 38.1 + - + -
191D LYS* 3.6 36.1 - - + -
193D PHE* 3.2 28.3 - + - -
314D PHE* 3.7 4.8 - - - +
329D GLY 3.1 0.8 - - - -
330D VAL* 1.3 90.8 - - + +
332D SER* 1.3 61.4 + - - +
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Residues in contact with SER 332 (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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3D EDO 2.8 1.2 + - - -
165D PHE* 4.7 1.6 - - - -
313D THR 3.3 9.6 - - - -
314D PHE 2.8 19.5 + - - -
315D PHE* 3.9 8.5 - - - -
328D SER* 3.2 23.5 - - - -
329D GLY 2.6 35.5 + - - +
330D VAL 4.2 4.5 - - - +
331D HIS* 1.3 80.2 - - - +
333D THR* 1.3 63.8 + - - +
334D ILE* 6.1 0.2 - - - -
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Residues in contact with THR 333 (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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162D LYS* 4.6 8.6 - - - -
165D PHE* 3.5 46.4 - - + -
178D HIS* 4.3 1.7 - - + +
311D ARG 3.5 4.4 + - - +
313D THR* 3.2 36.2 + - - +
315D PHE* 3.1 15.0 - - - -
331D HIS 4.2 1.3 - - - +
332D SER* 1.3 80.8 - - - +
334D ILE* 1.3 62.0 + - - +
335D LYS 4.2 0.4 - - - -
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Residues in contact with ILE 334 (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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282D PHE* 4.5 23.6 - - + -
295D GLY* 5.1 0.4 - - - -
296D VAL* 4.7 18.4 - - + +
298D ASN* 5.3 3.0 + - - +
300D ASP* 5.5 4.7 - - - +
301D THR* 3.8 29.0 - - + +
310D VAL* 3.6 28.7 - - + -
311D ARG 3.8 1.6 - - - +
312D LEU* 3.2 31.4 - - + -
315D PHE* 3.8 15.5 - - + -
333D THR* 1.3 77.3 - - - +
335D LYS* 1.3 61.9 + - - +
336D VAL* 4.4 2.8 + - + +
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Residues in contact with LYS 335 (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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300D ASP* 6.5 0.4 - - - -
310D VAL* 3.3 10.1 - - - +
311D ARG* 3.0 42.0 + - + +
333D THR 4.2 0.4 - - - -
334D ILE* 1.3 74.5 - - - +
336D VAL* 1.3 72.4 + - - +
337D ILE* 4.0 15.2 + - + -
4N C 3.5 31.0 + - - +
5N T 5.7 2.6 + - - -
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Residues in contact with VAL 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D PHE* 5.6 1.1 - - + -
300D ASP* 4.0 21.2 - - + +
301D THR* 4.1 10.8 - - - -
303D LYS* 4.4 2.5 - - + +
304D CYS* 3.7 50.0 - - + +
308D ASP* 4.5 0.7 - - - +
309D LYS 3.9 2.7 - - - +
310D VAL* 4.3 4.7 - - + -
334D ILE* 5.2 5.2 - - + +
335D LYS* 1.3 88.6 - - - +
337D ILE* 1.3 67.4 + - - +
338D LYS* 3.8 26.8 + - + +
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Residues in contact with ILE 337 (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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267D LEU* 3.9 17.7 - - + -
308D ASP* 3.2 5.4 - - - +
309D LYS* 2.9 48.4 + - + +
310D VAL* 4.3 2.2 - - - -
311D ARG* 4.5 2.2 - - + -
335D LYS* 4.0 20.9 - - + +
336D VAL* 1.3 79.8 - - - +
338D LYS* 1.3 68.0 + - - +
3N T 3.6 40.6 - - - +
4N C 3.2 29.4 - - - +
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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