Contacts of the strand formed by residues 298 - 307 (chain D) in PDB entry 2G4C
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 GLU 298 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D LEU* 3.7 26.4 - - + +
290D TYR* 2.9 10.5 - - - -
291D TYR 2.8 28.0 + - - -
293D PHE* 3.6 24.5 - - + -
295D TRP* 4.2 8.1 + - - +
296D GLY 4.4 0.9 - - - +
297D LYS* 1.3 79.4 - - - +
299D LEU* 1.3 71.4 + - - +
300D ILE* 3.5 1.9 + - - +
344D ARG* 3.6 35.8 + - - +
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Residues in contact with LEU 299 (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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288D LYS* 3.9 16.4 - - + -
289D LEU 3.4 7.2 - - - +
290D TYR* 3.3 25.6 - - + -
298D GLU* 1.3 79.5 + - - +
300D ILE* 1.3 62.2 + - - +
301D GLU* 3.3 29.8 - - - +
302D THR* 3.5 22.7 - - + -
341D ASP* 5.2 2.7 - - + +
344D ARG* 3.0 33.8 + - - +
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Residues in contact with ILE 300 (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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263D TRP* 3.4 48.1 - - + +
273D PHE* 3.5 22.0 - - + -
289D LEU* 3.0 20.5 + - + +
290D TYR 4.1 6.1 - - - +
291D TYR* 3.8 18.2 - - + -
293D PHE* 4.9 2.0 - - + -
298D GLU 3.6 11.0 - - - +
299D LEU* 1.3 80.3 - - - +
301D GLU* 1.3 62.4 + - + +
341D ASP* 2.7 37.7 + - - +
344D ARG* 4.2 20.9 - - + +
348D ALA* 5.1 5.4 - - + -
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Residues in contact with GLU 301 (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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114D TRP* 5.9 0.2 - - - -
259D ARG* 2.6 49.4 + - - +
263D TRP* 2.8 22.7 + - - -
289D LEU* 2.9 47.3 + - + +
299D LEU* 3.3 4.8 - - - +
300D ILE* 1.3 91.3 - - + +
302D THR* 1.3 80.9 + - - +
303D LEU* 4.2 0.3 - - - +
338D VAL* 3.4 10.3 - - + +
339D ASN 3.3 15.5 - - - +
340D GLY* 3.6 10.0 - - - -
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Residues in contact with THR 302 (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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287D ASN 3.7 8.1 - - - -
288D LYS* 3.8 16.8 - - + +
299D LEU* 3.5 29.4 - - + -
301D GLU* 1.3 85.2 - - - +
303D LEU* 1.3 63.7 + - - +
304D TRP* 4.5 16.6 - - - -
337D SER 3.7 3.3 - - - +
339D ASN* 2.9 38.2 + - - +
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Residues in contact with LEU 303 (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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252D LEU* 3.8 16.4 - - + +
255D TRP* 3.4 20.6 - - + +
256D LEU* 3.1 42.0 - - + +
259D ARG* 4.2 1.6 - - + -
286D GLY* 3.2 14.2 - - - -
287D ASN* 3.0 36.9 + - + +
289D LEU* 3.9 30.5 - - + -
301D GLU* 4.2 3.4 - - - +
302D THR* 1.3 73.1 - - - +
304D TRP* 1.3 67.6 + - - +
337D SER 3.4 4.9 - - - +
338D VAL* 3.7 20.6 - - + +
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Residues in contact with TRP 304 (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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252D LEU* 4.1 5.9 - - - +
278D CYS* 4.0 4.5 - - - -
279D GLN* 3.8 27.6 - - - -
280D ASP 4.5 1.1 - - - -
281D GLU* 3.2 39.6 + - + -
283D GLY 5.4 0.9 - - - -
284D ARG* 4.2 3.1 - - - -
285D LYS 3.1 49.6 - - - -
286D GLY* 3.2 10.1 - - - -
287D ASN 5.5 0.4 - - - -
288D LYS* 4.6 21.3 - - - +
302D THR* 4.5 20.5 - - - +
303D LEU* 1.3 82.8 + - - +
305D ASN* 1.3 64.1 + - - +
306D LEU* 3.6 19.8 + - + -
336D LEU* 3.1 8.8 - - - +
337D SER* 2.8 40.9 + - - +
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Residues in contact with ASN 305 (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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248D SER* 2.8 47.3 + - - -
249D ASN* 4.2 3.8 - - - +
252D LEU* 4.4 14.8 - - + +
283D GLY* 3.7 0.7 - - - -
284D ARG 3.6 26.2 + - - +
285D LYS* 3.3 21.4 + - + +
304D TRP* 1.3 75.1 - - - +
306D LEU* 1.3 60.2 + - - +
307D GLY* 3.0 23.0 + - - -
334D CYS* 4.0 3.1 - - - +
335D VAL 3.9 2.5 - - - +
336D LEU* 4.5 5.8 - - - +
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Residues in contact with LEU 306 (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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186D LEU* 3.4 34.1 - - + -
281D GLU* 4.0 21.3 - - + +
282D GLU* 3.0 22.1 - - + +
283D GLY* 3.6 11.8 - - - +
304D TRP* 3.6 26.5 - - + -
305D ASN* 1.3 73.4 - - - +
307D GLY* 1.3 62.9 + - - +
309D HIS* 3.6 7.4 + - - +
310D GLU* 3.4 27.1 - - + +
335D VAL* 2.9 34.7 + - + +
337D SER* 4.3 11.2 - - - -
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Residues in contact with GLY 307 (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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283D GLY* 5.5 0.7 - - - -
305D ASN* 3.0 11.4 + - - -
306D LEU* 1.3 81.4 - - - +
308D ASP* 1.3 60.5 + - - -
334D CYS* 3.2 27.1 - - - -
335D VAL* 2.9 32.6 + - - +
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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