Contacts of the helix formed by residues 308 - 326 (chain C) in PDB entry 2LDX
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 308 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C SER* 4.9 4.9 - - - -
221C LYS* 5.1 0.4 - - - +
306C ASN 3.5 3.4 + - - -
307C MET* 1.3 73.2 - - - +
309C ALA* 1.3 83.3 + - - +
310C GLU* 2.9 30.0 + - - +
311C GLU* 2.6 50.8 + - + +
312C GLU* 2.9 5.6 + - - -
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Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C MET 4.0 0.4 + - - -
308C THR* 1.3 79.5 + - - +
310C GLU* 1.3 58.4 + - + +
312C GLU* 3.0 16.6 - - - +
313C GLY* 2.9 15.1 + - - -
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Residues in contact with GLU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C LYS* 2.6 31.4 + - - +
308C THR* 2.7 29.1 + - - +
309C ALA* 1.3 72.3 - - + +
311C GLU* 1.3 62.1 + - - +
312C GLU 2.8 2.2 - - - -
313C GLY* 2.5 24.1 + - - +
314C LEU* 2.5 43.9 + - + +
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Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C VAL* 4.3 16.8 - - + +
199C ILE* 4.0 24.9 - - + +
200C TRP* 3.9 9.5 + - - +
201C SER* 2.9 44.5 + - - -
221C LYS* 4.8 9.0 + - - +
307C MET* 3.1 28.6 - - + -
308C THR* 2.6 37.0 + - + +
310C GLU* 1.3 84.5 + - - +
312C GLU* 1.3 52.2 + - - -
314C LEU* 3.4 2.1 + - - +
315C LEU* 2.9 27.0 + - - +
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Residues in contact with GLU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C HIS* 3.6 44.2 + - + +
307C MET* 3.2 23.1 - - + +
308C THR 2.9 7.9 + - - +
309C ALA* 3.0 17.0 - - - +
311C GLU* 1.3 74.5 - - - +
313C GLY* 1.3 53.8 + - - +
315C LEU* 4.5 0.9 - - - -
316C LYS* 2.7 57.3 + - + +
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Residues in contact with GLY 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C ALA 2.9 5.7 + - - -
310C GLU* 2.5 25.6 + - - -
312C GLU* 1.3 67.4 - - - +
314C LEU* 1.3 56.9 + - - -
316C LYS* 2.8 31.0 + - - +
317C LYS* 2.8 13.2 + - - +
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C SER 6.0 0.7 - - - +
196C SER 5.7 1.1 - - - +
197C VAL* 3.9 32.8 - - + -
198C PRO* 6.0 0.7 - - + -
221C LYS* 5.6 9.2 - - - +
310C GLU* 2.5 52.6 + - + +
311C GLU* 3.8 3.8 - - - +
313C GLY* 1.3 67.2 - - - -
315C LEU* 1.3 55.7 - - - +
317C LYS* 2.6 46.6 + - + +
318C SER* 2.8 8.6 + - - -
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Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LEU* 3.4 33.9 - - + -
190C GLY* 3.8 9.4 - - - +
197C VAL* 3.8 16.5 - - + +
199C ILE* 4.9 0.2 - - + -
280C HIS* 3.6 28.0 - - + +
288C LEU* 3.3 35.7 - - + -
290C ILE* 4.1 6.5 - - + -
307C MET* 4.3 22.0 - - + -
311C GLU 2.9 19.5 + - - +
312C GLU* 4.1 1.8 - - - +
314C LEU* 1.3 72.5 - - - +
316C LYS* 1.3 63.8 + - - +
317C LYS 2.8 1.7 + - - -
318C SER* 3.0 13.6 + - - +
319C ALA* 3.1 13.2 + - - +
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Residues in contact with LYS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C HIS* 3.2 33.8 - - + +
281C GLY* 3.6 17.7 - - - -
282C ILE* 4.3 5.9 - - + +
312C GLU* 2.7 47.3 + - - +
313C GLY* 2.8 11.1 + - - +
315C LEU* 1.3 71.4 - - - +
317C LYS* 1.3 55.2 - - - +
319C ALA* 3.1 18.0 - - - +
320C ASP* 3.6 15.8 + - - +
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Residues in contact with LYS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C SER* 6.1 6.3 - - - +
313C GLY 2.8 10.1 + - - +
314C LEU* 2.6 30.4 + - + +
316C LYS* 1.3 69.1 - - - +
318C SER* 1.3 70.7 + - - +
320C ASP* 3.2 8.0 + - - +
321C THR* 3.0 25.1 + - - +
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Residues in contact with SER 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C GLY* 4.1 8.7 - - - -
191C GLU* 3.7 16.3 + - - -
195C SER* 3.0 40.7 + - - -
197C VAL* 5.6 0.2 - - - +
288C LEU* 5.0 1.3 - - - -
314C LEU 2.8 13.9 + - - -
315C LEU* 3.0 6.6 + - - -
317C LYS* 1.3 71.7 - - - +
319C ALA* 1.3 69.9 + - - +
321C THR* 2.5 26.4 + - - -
322C LEU* 2.9 17.9 + - - -
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C ILE* 3.1 48.9 - - + -
286C VAL* 3.1 30.3 - - - +
288C LEU* 4.7 5.0 - - - +
315C LEU 3.1 3.1 + - - +
316C LYS 3.1 15.0 - - - +
318C SER* 1.3 76.0 - - - +
320C ASP* 1.3 53.4 - - - +
322C LEU* 3.2 2.8 - - - +
323C TRP 2.8 27.0 + - - -
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Residues in contact with ASP 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ILE* 5.3 3.3 - - - +
284C GLU* 5.8 2.1 - - - +
286C VAL* 5.1 1.6 - - - +
316C LYS 3.6 12.8 - - - +
317C LYS* 3.2 9.3 + - - +
318C SER 2.6 3.8 + - - -
319C ALA* 1.3 77.6 - - - +
321C THR* 1.3 71.9 + - - +
323C TRP* 2.5 34.8 + - - +
324C ASN 3.1 4.7 + - - -
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Residues in contact with THR 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 5.4 6.7 - - + -
191C GLU* 5.4 2.9 - - - +
195C SER* 5.0 11.0 + - - +
317C LYS* 3.0 24.8 + - - +
318C SER* 2.5 19.8 + - - -
320C ASP* 1.3 73.8 - - - +
322C LEU* 1.3 57.3 + - - +
323C TRP 2.7 7.6 + - - -
324C ASN* 3.3 8.5 + - - +
325C MET* 3.6 27.0 + - + +
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Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 5.1 0.2 - - + -
140C ASP* 3.6 22.2 - - + +
141C ILE* 3.3 39.3 - - + +
191C GLU* 4.4 24.5 - - + +
286C VAL* 4.1 6.7 - - + -
287C PHE 3.5 10.8 - - - +
288C LEU* 3.4 34.5 - - + -
318C SER* 2.9 9.4 + - - +
319C ALA 3.2 12.1 - - - +
321C THR* 1.3 81.4 - - - +
323C TRP* 1.3 55.5 + - - +
325C MET* 3.4 12.8 - - - +
326C GLN* 2.9 30.0 + - - +
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Residues in contact with TRP 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C TYR* 4.8 7.0 - - - -
284C GLU* 3.3 42.1 + - + +
285C GLU* 4.2 19.7 - - + -
286C VAL* 3.4 22.0 - - + -
319C ALA 2.8 13.9 + - - +
320C ASP* 2.5 36.1 + - + +
322C LEU* 1.3 66.9 - - - +
324C ASN* 1.3 87.2 + - + +
325C MET 3.0 1.1 - - - -
326C GLN* 2.9 42.7 + - + +
327C LYS* 5.9 1.8 - - + -
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Residues in contact with ASN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ASP 3.1 9.5 + - - -
321C THR 3.3 1.5 + - - +
323C TRP* 1.3 88.5 + - + +
325C MET* 1.3 54.5 - - - +
326C GLN 2.4 0.9 + - - -
327C LYS* 2.4 71.4 + - + +
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Residues in contact with MET 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 3.3 47.6 - - + +
109C LEU* 4.3 19.5 - - + +
110C GLN* 5.8 0.2 - - - +
141C ILE* 3.9 18.1 - - + +
321C THR* 3.6 24.4 + - + +
322C LEU* 3.4 14.8 - - - +
324C ASN* 1.3 75.4 - - - +
326C GLN* 1.3 55.1 + - - +
327C LYS* 3.2 18.9 + - - +
328C ASN* 3.0 21.3 + - - -
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE* 4.3 12.1 - - + +
144C TYR* 3.1 60.3 + - + +
285C GLU 3.1 9.9 - - - +
286C VAL* 3.9 17.4 - - - +
287C PHE 4.1 7.1 + - - +
322C LEU* 2.9 37.9 + - - +
323C TRP* 3.2 30.0 - - + +
324C ASN 2.4 7.0 + - - -
325C MET* 1.3 68.0 - - - +
327C LYS* 1.3 49.9 + - - -
328C ASN* 2.7 29.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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