Contacts of the helix formed by residues 2221 - 2233 (chain B) in PDB entry 2DQZ
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 SER2221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B PLM 3.3 12.0 + - - +
2101B PHE* 5.4 2.0 - - - -
2141B GLY* 4.3 2.7 - - - -
2142B GLY 4.6 0.4 - - - -
2220B GLU* 1.3 88.6 - - - +
2222B ALA* 1.3 57.1 + - - -
2223B GLY 2.9 3.6 - - - -
2224B GLY* 2.5 22.2 + - - -
2225B GLU* 2.8 11.8 + - - +
2246B GLU 2.8 12.9 + - - -
2247B SER 3.2 15.9 - - - -
2248B GLY* 3.9 4.9 - - - -
2255B LEU* 4.7 1.8 - - - -
2468B HIS* 2.9 22.8 + - - -
4001B F 2.4 23.3 - - - -
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Residues in contact with ALA2222 (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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2140B HIS 4.4 0.9 - - - -
2141B GLY* 4.0 2.0 - - - -
2142B GLY 3.8 4.5 - - - +
2143B GLY* 3.3 16.6 - - - +
2144B LEU* 3.4 28.6 - - + +
2170B TYR* 4.6 0.9 - - - +
2220B GLU 3.3 0.2 + - - -
2221B SER* 1.3 71.6 - - - +
2223B GLY* 1.3 56.4 + - - +
2225B GLU* 3.6 3.9 - - - +
2226B SER* 2.9 31.9 + - - -
2255B LEU* 3.6 15.0 - - + +
4001B F 2.6 26.4 - - - -
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Residues in contact with GLY2223 (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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2139B ILE* 3.3 31.9 - - - +
2140B HIS 3.4 7.6 - - - -
2141B GLY* 3.6 3.8 - - - -
2219B GLY* 3.7 7.7 - - - -
2220B GLU 2.9 8.2 + - - -
2222B ALA* 1.3 77.1 - - - +
2224B GLY* 1.3 65.0 + - - +
2226B SER* 3.3 3.5 + - - -
2227B VAL* 3.1 27.2 + - - +
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Residues in contact with GLY2224 (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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2219B GLY 3.4 16.8 - - - -
2220B GLU 3.4 6.3 - - - -
2221B SER 2.5 18.5 + - - -
2223B GLY* 1.3 69.5 - - - +
2225B GLU* 1.3 59.3 + - - -
2227B VAL* 2.9 17.4 + - - +
2228B SER 3.1 2.4 + - - -
2245B SER* 2.7 22.0 + - - -
2246B GLU 4.3 2.9 - - - -
2248B GLY 3.1 15.4 - - - +
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Residues in contact with GLU2225 (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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2144B LEU* 4.2 4.8 - - - +
2191B HIS* 3.7 7.6 - - - -
2221B SER 2.8 6.1 + - - +
2222B ALA 3.6 6.8 - - - +
2224B GLY* 1.3 74.4 - - - +
2226B SER* 1.3 65.9 + - - +
2228B SER* 3.3 2.9 + - - -
2229B VAL* 2.9 37.2 + - - +
2248B GLY* 3.3 3.4 + - - -
2249B VAL* 3.3 36.3 - - - +
2250B ALA* 4.0 4.9 - - - -
2255B LEU* 3.4 49.1 - - + +
2256B VAL* 3.6 9.8 - - + +
2321B THR* 2.7 23.6 + - - -
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Residues in contact with SER2226 (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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2139B ILE* 4.1 5.1 - - - +
2144B LEU* 4.0 5.0 - - - +
2170B TYR* 4.8 0.2 + - - -
2191B HIS* 3.6 14.2 + - - -
2194B GLN* 3.1 36.0 + - - -
2222B ALA 2.9 23.3 + - - -
2223B GLY* 3.4 9.7 - - - -
2224B GLY 3.1 0.2 - - - -
2225B GLU* 1.3 77.5 + - - +
2227B VAL* 1.3 60.8 + - - +
2229B VAL* 3.3 7.0 + - - +
2230B LEU* 2.8 36.1 + - - +
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Residues in contact with VAL2227 (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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2139B ILE* 4.2 13.0 - - + -
2217B ILE* 3.8 13.7 - - + +
2218B PHE* 4.0 8.7 - - - +
2219B GLY 3.7 21.5 - - - +
2223B GLY 3.1 15.6 + - - +
2224B GLY* 2.9 9.0 + - - +
2226B SER* 1.3 76.9 - - - +
2228B SER* 1.3 62.6 + - - +
2230B LEU* 3.1 5.0 + - - +
2231B VAL* 2.9 26.7 + - - +
2243B ALA* 3.5 30.5 - - + -
2244B ILE 3.8 13.7 - - - +
2245B SER* 3.7 8.5 - - - +
2346B TYR* 4.1 4.3 - - + -
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Residues in contact with SER2228 (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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2224B GLY 3.1 5.6 + - - -
2225B GLU 3.5 3.4 - - - -
2227B VAL* 1.3 77.9 - - - +
2229B VAL* 1.3 61.0 + - - +
2231B VAL* 3.2 16.7 + - - +
2232B LEU* 3.3 19.1 + - - +
2249B VAL* 3.7 11.8 - - - +
2250B ALA* 2.9 41.7 + - - +
2346B TYR* 3.6 20.6 + - - -
2433B VAL* 4.5 10.2 - - - +
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Residues in contact with VAL2229 (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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2191B HIS* 4.5 6.7 - - + +
2225B GLU* 2.9 40.9 + - - +
2226B SER* 3.5 9.2 - - - +
2228B SER* 1.3 77.8 - - - +
2230B LEU* 1.3 63.5 + - + +
2232B LEU* 3.1 9.5 + - - +
2233B SER* 3.0 19.9 + - - -
2250B ALA* 4.2 14.6 - - + -
2256B VAL* 5.3 1.8 - - + -
2321B THR* 4.2 13.5 - - + +
2327B LEU* 3.5 31.9 - - + -
2328B LEU* 3.9 18.7 - - + +
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Residues in contact with LEU2230 (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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2139B ILE* 3.9 26.7 - - + -
2191B HIS* 4.4 3.4 - - + +
2194B GLN* 4.2 17.7 - - + +
2195B VAL* 3.6 32.1 - - + +
2198B LEU* 4.2 15.7 - - + -
2217B ILE* 4.2 19.1 - - + -
2226B SER 2.8 20.7 + - - +
2227B VAL 3.1 4.2 + - - +
2229B VAL* 1.3 78.0 - - + +
2231B VAL* 1.3 61.0 + - - +
2232B LEU 3.1 1.1 + - - -
2233B SER* 3.4 12.4 + - - +
2236B ALA* 3.5 29.8 - - + +
2240B PHE* 3.7 6.0 - - + -
2327B LEU* 4.6 9.0 - - + -
2341B PHE* 5.1 0.3 - - - -
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Residues in contact with VAL2231 (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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2217B ILE* 4.6 0.4 - - + -
2227B VAL* 2.9 26.8 + - + +
2228B SER* 3.4 12.1 - - - +
2229B VAL 3.2 0.4 - - - -
2230B LEU* 1.3 76.9 - - - +
2232B LEU* 1.3 63.1 + - + +
2240B PHE* 3.9 17.0 - - + -
2243B ALA* 3.8 27.4 - - + -
2341B PHE* 3.2 21.7 - - - -
2342B HIS 5.0 4.0 - - - +
2343B THR* 6.5 0.4 - - - -
2344B VAL* 5.1 10.1 - - + +
2346B TYR* 4.5 22.7 - - + -
2437B HIS* 5.0 10.8 - - + -
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Residues in contact with LEU2232 (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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2228B SER* 3.4 16.8 - - - +
2229B VAL* 3.1 8.8 + - - +
2231B VAL* 1.3 85.9 - - + +
2233B SER* 1.3 59.5 + - - +
2234B PRO* 3.8 5.4 - - - +
2250B ALA* 3.9 23.8 - - + -
2328B LEU* 4.1 6.1 - - + -
2332B PRO* 4.0 22.9 - - + +
2335B LEU* 3.7 31.6 - - + +
2336B GLN* 4.0 38.4 - - + +
2341B PHE* 3.8 15.3 - - + -
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Residues in contact with SER2233 (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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2229B VAL 3.0 14.0 + - - -
2230B LEU* 3.4 15.3 + - - +
2232B LEU* 1.3 78.4 - - - +
2234B PRO* 1.3 67.4 - - - +
2235B LEU* 3.1 12.7 + - - +
2236B ALA* 3.4 10.1 + - - -
2237B LYS 3.7 4.0 + - - -
2327B LEU* 2.6 51.5 + - - +
2328B LEU* 4.4 0.9 - - - -
2341B PHE* 3.2 11.5 - - - -
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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