Contacts of the helix formed by residues 289 - 305 (chain B) in PDB entry 2D4H
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 ASN 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE 3.7 6.3 + - - +
35B THR* 4.0 15.0 + - - +
36B GLN 3.6 24.5 - - - +
37B PRO* 4.6 1.1 - - + -
38B MET* 3.4 8.1 - - - -
287B GLN 4.2 5.5 - - - +
288B VAL* 1.3 73.2 - - - +
290B GLY* 1.3 57.4 + - - +
291B PRO* 3.1 23.7 - - - +
292B ARG* 2.8 39.9 + - - +
293B LEU* 2.8 32.9 + - - +
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 2.8 32.8 - - - +
34B ILE* 2.8 19.6 + - - -
36B GLN 4.4 0.4 + - - -
38B MET* 3.5 17.4 - - - +
289B ASN* 1.3 73.2 - - - +
291B PRO* 1.3 64.3 - - - +
293B LEU 3.4 0.2 + - - -
294B GLU* 3.1 19.1 + - - +
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Residues in contact with PRO 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 5.9 7.0 - - - +
295A SER* 4.7 2.3 + - - -
31B LEU 3.7 0.4 - - - +
32B SER* 3.7 19.5 - - - +
34B ILE 3.4 7.6 - - - +
35B THR* 5.3 2.9 - - + -
289B ASN* 3.1 21.8 - - - +
290B GLY* 1.3 80.2 - - - +
292B ARG* 1.3 78.0 + - - +
294B GLU* 3.2 16.5 + - - +
295B SER* 2.8 35.9 + - - -
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO* 3.4 35.4 - - - +
292A ARG* 5.8 3.0 - - - +
282B LEU* 4.3 23.3 - - + +
286B ILE* 4.8 7.0 - - + -
287B GLN 4.5 3.6 - - - +
288B VAL* 3.8 14.1 - - + -
289B ASN* 2.8 53.4 + - - +
291B PRO* 1.3 101.2 - - - +
293B LEU* 1.3 60.3 + - - +
295B SER* 3.5 8.6 + - - -
296B LEU* 3.2 26.6 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 5.4 4.5 - - + -
31B LEU* 3.7 29.2 - - + -
38B MET* 4.3 10.1 - - - -
40B VAL* 3.8 12.3 - - + -
94B VAL* 4.2 20.2 - - + -
96B LEU* 5.6 1.3 - - + -
122B LEU* 3.6 36.6 - - + +
280B LYS* 4.9 0.9 - - + -
288B VAL* 3.5 18.5 - - + +
289B ASN 2.8 19.5 + - - +
290B GLY 3.8 3.6 - - - +
292B ARG* 1.3 69.9 - - - +
294B GLU* 1.3 61.8 + - - +
296B LEU* 3.2 9.7 + - + +
297B VAL* 2.9 39.3 + - + +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER* 4.0 18.8 + - - -
299A THR* 5.1 1.0 + - - -
28B LEU* 3.7 38.6 - - + +
31B LEU* 3.7 14.5 - - + +
32B SER* 3.5 26.2 + - - -
290B GLY 3.1 14.5 + - - +
291B PRO* 3.3 14.8 - - - +
293B LEU* 1.3 76.3 - - - +
295B SER* 1.3 55.5 + - - +
297B VAL* 3.4 5.2 + - - +
298B LEU* 2.9 45.4 + - + +
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO 4.9 1.7 + - - -
294A GLU* 3.8 26.6 + - - +
295A SER* 4.0 17.6 + - - -
298A LEU* 3.8 7.1 - - - +
291B PRO 2.8 19.1 + - - -
292B ARG* 3.6 10.8 - - - -
294B GLU* 1.3 74.8 - - - +
296B LEU* 1.3 50.4 + - - +
298B LEU* 3.3 6.5 + - - +
299B THR* 2.6 40.6 + - - -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU 5.7 0.4 - - - +
122B LEU* 4.1 6.5 - - + -
280B LYS* 4.7 14.1 - - - -
282B LEU* 4.0 22.2 - - + -
288B VAL* 3.9 24.7 - - + -
292B ARG 3.2 15.4 + - - +
293B LEU* 3.2 16.2 + - + +
295B SER* 1.3 76.5 - - - +
297B VAL* 1.3 56.3 + - - +
299B THR* 3.4 8.6 - - + +
300B TYR* 2.8 78.8 + - + +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.2 17.3 - - + -
14B ILE* 4.1 26.2 - - + -
23B ALA* 4.5 6.5 - - + -
28B LEU* 3.9 20.2 - - + -
31B LEU* 4.5 7.9 - - + -
118B LEU* 5.2 0.2 - - - -
122B LEU* 3.7 30.2 - - + +
293B LEU* 2.9 21.9 + - + +
294B GLU 3.6 7.0 - - - +
296B LEU* 1.3 74.3 - - - +
298B LEU* 1.3 62.8 + - - +
300B TYR* 4.3 1.3 - - - +
301B VAL* 3.1 37.9 + - + +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER* 3.5 30.1 - - - +
298A LEU* 3.4 18.1 - - + +
299A THR* 3.2 37.7 - - + +
302A ASN* 4.9 14.8 - - - +
23B ALA* 5.2 3.4 - - + -
28B LEU* 3.9 27.4 - - + -
294B GLU* 2.9 35.1 + - + +
295B SER* 3.6 5.4 - - - +
297B VAL* 1.3 77.2 - - - +
299B THR* 1.3 58.1 + - - +
301B VAL* 5.2 2.5 - - - -
302B ASN* 3.1 27.9 + - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 5.6 2.8 - - + +
294A GLU* 5.0 3.3 + - - -
298A LEU* 3.4 23.4 - - + +
156B SER* 3.5 32.4 - - - +
295B SER* 2.6 28.5 + - - -
296B LEU* 3.1 15.8 + - + +
298B LEU* 1.3 76.2 - - - +
300B TYR* 1.3 64.2 + - + +
302B ASN* 3.7 2.9 + - - +
303B ALA* 3.1 25.5 + - - +
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.6 18.8 - - + -
121B LEU* 3.6 50.3 + - + +
122B LEU* 3.7 18.2 - - + -
152B ILE* 3.5 20.4 - - + +
153B ARG* 4.3 15.0 + - + +
156B SER* 3.7 20.2 - - - -
174B PHE* 4.8 3.5 - - - -
296B LEU* 2.8 55.8 + - + +
297B VAL 4.3 0.2 - - - +
299B THR* 1.3 77.9 - - + +
301B VAL* 1.3 60.2 + - - +
302B ASN 3.2 1.3 - - - -
303B ALA* 3.1 3.5 + - - +
304B ILE* 2.9 36.0 + - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASN* 4.3 21.1 - - - +
14B ILE* 3.8 35.0 - - + -
21B LEU* 4.1 31.6 - - + +
22B MET 4.8 0.4 - - - +
23B ALA* 4.7 12.1 - - + +
118B LEU* 3.9 12.8 - - + -
297B VAL* 3.1 21.8 + - + +
298B LEU* 4.9 1.8 - - - +
300B TYR* 1.3 75.0 - - - +
302B ASN* 1.3 57.0 + - - +
304B ILE* 3.5 3.5 + - - +
305B SER* 2.9 31.6 + - - -
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Residues in contact with ASN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.9 9.1 + - - +
298A LEU* 4.2 16.7 - - + +
301A VAL* 3.5 30.0 - - - +
302A ASN* 3.6 27.7 + - + -
305A SER* 4.0 5.3 + - - -
155B LYS* 5.6 4.6 - - - +
298B LEU 3.1 21.9 + - - +
299B THR 3.7 3.9 + - - +
300B TYR 3.2 0.2 - - - -
301B VAL* 1.3 80.0 - - - +
303B ALA* 1.3 58.9 + - - +
305B SER* 3.2 4.2 - - - +
306B SER* 3.0 36.1 + - - -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 4.0 20.2 - - + -
155B LYS* 3.7 31.3 - - + +
156B SER* 4.1 10.8 - - - -
299B THR 3.1 19.3 + - - +
300B TYR 3.1 5.1 + - - +
302B ASN* 1.3 76.1 - - - +
304B ILE* 1.3 66.5 + - - +
306B SER* 3.2 16.1 - - - -
307B GLY 4.7 0.2 + - - -
309B LEU* 5.1 6.4 + - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.2 14.6 - - + -
111B ASN* 5.2 0.9 - - - +
114B TRP* 3.6 53.4 - - + +
118B LEU* 3.5 38.1 - - + -
152B ILE* 3.7 30.7 - - + -
300B TYR 2.9 18.8 + - - +
301B VAL* 3.9 3.4 - - - +
303B ALA* 1.3 75.7 - - - +
305B SER* 1.3 60.3 - - - +
306B SER 3.0 6.1 + - - -
307B GLY* 3.8 6.6 + - - -
309B LEU* 4.2 14.5 - - - +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.2 14.0 + - - -
302A ASN* 5.0 8.1 - - - -
305A SER* 3.8 6.8 + - - -
20B ARG* 3.0 44.8 + - - +
21B LEU* 4.5 15.3 + - - +
301B VAL* 2.9 22.6 + - - -
302B ASN* 3.2 7.0 - - - +
304B ILE* 1.3 75.8 - - - +
306B SER* 1.3 56.4 + - - +
307B GLY 3.5 1.6 - - - +
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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
------------------------------------------------------------
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