Contacts of the helix formed by residues 319 - 336 (chain P) in PDB entry 2D2I
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 319 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ARG* 2.7 56.4 + - + +
13P ILE* 4.1 6.0 - - + +
16P ASN* 3.5 17.2 + - - +
52P VAL* 4.3 4.6 - - - +
53P LEU* 5.5 0.5 - - - +
240P PRO 4.5 1.7 - - - +
241P ASN* 3.3 30.7 + - - +
317P ASP* 3.0 3.1 + - - +
318P ASN* 1.3 81.4 - - - +
320P TRP* 1.3 60.9 + - + +
322P TYR* 4.1 0.5 - - - +
323P SER* 2.6 36.5 + - - -
4341P NAP 3.6 19.9 + - - +
191Q LEU* 4.0 14.9 - - - +
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Residues in contact with TRP 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P ASN* 3.4 24.2 - - - +
19P ARG* 3.9 27.1 - - + -
20P CYS* 3.7 33.0 - - - -
23P GLY* 6.2 1.1 - - - -
53P LEU* 3.5 23.3 - - + -
241P ASN* 5.5 0.9 - - - +
290P GLY* 3.4 32.8 + - - -
291P THR 3.5 9.4 - - - -
292P ASP* 2.9 22.4 + - - -
317P ASP* 3.0 19.2 + - - +
319P GLU* 1.3 77.7 - - - +
321P GLY* 1.3 67.2 + - - +
323P SER* 3.3 2.9 + - - -
324P GLN* 3.0 39.1 + - + +
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Residues in contact with GLY 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291P THR 3.7 17.3 - - - -
292P ASP 3.8 9.9 - - - -
293P GLU 4.1 8.1 - - - -
294P SER* 5.4 2.5 - - - -
316P TYR* 6.4 0.2 - - - -
317P ASP* 3.0 14.6 + - - +
320P TRP* 1.3 79.4 - - - +
322P TYR* 1.3 62.0 + - - +
324P GLN* 3.1 14.3 + - - +
325P ARG* 3.2 20.5 + - - +
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Residues in contact with TYR 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ILE* 4.0 11.0 - - + -
122P THR* 2.9 33.7 - - - -
123P ALA 3.3 0.2 + - - -
152P ASN* 3.6 13.2 - - + +
153P ALA 2.7 30.1 + - - -
154P SER 3.6 9.2 - - - -
155P CYS* 3.5 22.2 - - + -
158P ASN* 3.7 18.6 - - + -
317P ASP 3.6 4.8 + - - -
318P ASN* 3.3 21.5 - - - +
319P GLU 4.1 1.1 - - - +
321P GLY* 1.3 76.4 - - - +
323P SER* 1.3 56.2 + - - +
325P ARG* 2.7 30.1 + - + +
326P VAL* 2.9 34.7 + - + +
4341P NAP 3.3 28.3 - + - -
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Residues in contact with SER 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ILE* 3.7 19.8 - - - +
16P ASN* 3.3 23.5 - - - +
17P PHE* 3.8 13.6 - - - +
20P CYS* 3.9 6.5 - - - -
319P GLU 2.6 23.2 + - - -
320P TRP 3.7 4.0 - - - -
321P GLY 3.3 0.2 - - - -
322P TYR* 1.3 79.4 - - - +
324P GLN* 1.3 62.2 + - - +
326P VAL* 3.7 11.6 - - - +
327P VAL* 3.1 27.9 + - - +
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Residues in contact with GLN 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P CYS* 3.5 21.1 + - - +
23P GLY 6.2 0.4 - - - -
24P ARG* 2.6 56.3 + - - +
292P ASP* 3.6 36.1 + - + +
320P TRP* 3.0 39.0 + - + +
321P GLY 3.1 9.4 + - - +
323P SER* 1.3 76.6 - - - +
325P ARG* 1.3 74.4 + - - +
327P VAL* 3.4 0.4 + - - -
328P ASP* 2.9 24.8 + - - -
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Residues in contact with ARG 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P ARG* 5.0 1.2 - - - +
135P ILE* 3.9 24.2 - - + +
152P ASN* 3.1 15.0 - - - +
158P ASN* 3.7 20.6 - - + +
274P GLY 3.9 10.5 + - - -
275P ILE* 3.8 14.9 - - - +
292P ASP* 2.9 32.1 + - - +
293P GLU* 3.7 1.6 - - - +
294P SER* 3.0 36.1 + - - +
321P GLY 3.2 11.0 + - - +
322P TYR* 2.7 15.3 + - + +
324P GLN* 1.3 87.9 - - - +
326P VAL* 1.3 57.8 + - - +
328P ASP* 2.9 33.6 + - - +
329P LEU* 2.9 24.4 + - - +
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Residues in contact with VAL 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ILE* 4.7 2.2 - - + -
17P PHE* 3.1 34.8 - - + -
96P ILE* 4.6 5.8 - - + -
120P LEU* 3.9 9.2 - - + +
122P THR* 4.2 22.4 - - + -
152P ASN* 3.0 17.0 + - + +
322P TYR* 2.9 40.9 + - + +
323P SER* 3.7 9.4 - - - +
324P GLN 3.4 0.2 - - - -
325P ARG* 1.3 71.6 - - - +
327P VAL* 1.3 59.9 + - - +
329P LEU* 3.2 2.9 + - - +
330P ALA* 2.8 30.7 + - - +
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Residues in contact with VAL 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P PHE* 3.4 42.2 - - + +
20P CYS* 3.9 11.4 - - + -
21P TRP* 4.1 11.7 - - + +
24P ARG* 3.5 40.2 - - + +
29P LEU* 4.3 2.2 - - + +
323P SER 3.1 18.1 + - - +
324P GLN 3.5 7.4 - - - +
326P VAL* 1.3 77.5 - - - +
328P ASP* 1.3 52.4 + - - +
330P ALA* 3.7 2.3 - - - +
331P GLU* 2.8 46.1 + - - +
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Residues in contact with ASP 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P ARG* 2.8 26.3 + - - -
135P ILE* 3.8 23.2 - - + +
275P ILE* 5.0 0.9 - - - +
324P GLN 2.9 12.9 + - - -
325P ARG* 2.9 41.9 + - - +
327P VAL* 1.3 73.9 - - - +
329P LEU* 1.3 60.7 + - - +
331P GLU* 3.3 8.2 - - - +
332P LEU* 2.9 26.9 + - - +
335P ARG* 4.5 3.5 + - - -
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Residues in contact with LEU 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P LEU* 3.5 32.8 - - + -
133P TYR* 4.2 28.3 - - + +
135P ILE* 4.0 13.2 - - + +
142P TYR* 4.8 4.0 - - + -
150P ILE* 4.1 14.6 - - + -
151P SER 3.8 17.5 - - - +
152P ASN* 3.8 16.2 - - - +
325P ARG 2.9 12.1 + - - +
326P VAL 3.6 7.0 - - - +
328P ASP* 1.3 73.6 - - - +
330P ALA* 1.3 61.8 + - - +
332P LEU* 2.9 23.3 + - + +
333P ALA* 2.8 27.5 + - - +
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Residues in contact with ALA 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P ILE* 4.2 2.1 - - - +
17P PHE* 4.6 2.2 - - + -
29P LEU* 3.5 26.2 - - + +
94P LEU* 3.8 22.4 - - + -
96P ILE* 4.5 9.4 - - + -
120P LEU* 3.8 11.8 - - + +
326P VAL 2.8 20.6 + - - +
327P VAL* 3.7 6.3 - - - +
329P LEU* 1.3 72.8 - - - +
331P GLU* 1.3 61.8 + - - +
333P ALA* 3.3 6.1 + - - +
334P ALA 3.1 17.2 + - - -
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Residues in contact with GLU 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P TRP* 4.4 0.7 - - - -
24P ARG* 4.9 12.6 + - - +
26P ASN 4.4 4.0 - - - +
27P THR* 2.7 31.0 + - - -
28P ASP* 2.6 38.1 + - - +
29P LEU* 3.4 15.6 - - - +
327P VAL* 2.8 26.0 + - - +
328P ASP* 3.3 10.1 - - - +
330P ALA* 1.3 77.3 - - - +
332P LEU* 1.3 57.6 + - - +
334P ALA* 3.2 4.9 + - - +
335P ARG* 3.0 43.3 + - - +
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Residues in contact with LEU 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P ILE* 4.7 4.0 - - + -
139P ASP* 3.9 26.7 - - + +
142P TYR* 3.6 38.1 - - + -
328P ASP 2.9 13.9 + - - +
329P LEU* 2.9 21.7 + - + +
331P GLU* 1.3 74.5 - - - +
333P ALA* 1.3 66.6 + - - +
335P ARG* 3.0 26.3 + - - +
336P LYS* 2.9 45.9 + - + +
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Residues in contact with ALA 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P ILE* 4.7 3.4 - - + -
94P LEU* 4.8 11.7 - - + -
118P LYS* 5.2 6.5 - - + -
142P TYR* 3.6 31.3 + - + +
144P HIS* 4.9 2.4 - - + -
150P ILE* 4.8 9.6 - - + -
329P LEU 2.8 15.6 + - - +
330P ALA* 3.3 11.2 + - - +
332P LEU* 1.3 73.9 - - - +
334P ALA* 1.3 52.9 + - - +
336P LYS 3.2 1.9 + - - -
337P SER* 2.8 36.1 + - - -
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Residues in contact with ALA 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P MET* 4.2 16.3 - - - +
3P ILE* 3.4 33.6 - - + +
28P ASP* 3.6 29.2 - - + +
29P LEU* 3.6 4.9 - - + -
330P ALA 3.1 8.8 + - - +
331P GLU 3.4 8.5 - - - +
332P LEU 3.1 0.4 - - - -
333P ALA* 1.3 78.9 - - - +
335P ARG* 1.3 62.2 + - - +
336P LYS 3.3 0.3 + - - -
337P SER* 3.3 13.2 + - - +
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Residues in contact with ARG 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P MET* 5.6 6.6 - - - +
28P ASP* 3.2 26.7 + - - +
328P ASP 4.5 4.0 + - - -
331P GLU* 3.0 22.1 + - - +
332P LEU* 3.0 41.7 + - - +
334P ALA* 1.3 76.6 - - - +
336P LYS* 1.3 77.3 + - + +
337P SER 4.9 1.2 - - - +
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Residues in contact with LYS 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142P TYR* 4.0 30.4 + - + +
143P ARG* 5.9 0.2 - - - -
144P HIS* 3.1 22.7 - - + +
332P LEU* 2.9 36.8 + - + +
333P ALA 3.3 2.5 - - - -
335P ARG* 1.3 98.6 - - + +
337P SER* 1.3 65.6 + - - +
338P GLY* 4.6 0.2 - - - -
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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