Contacts of the helix formed by residues 249 - 257 (chain K) in PDB entry 5LN3
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 ASP 249 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129K SER* 4.4 9.2 + - - -
145K PRO* 4.1 11.0 - - + +
146K GLU 3.3 25.3 + - - +
147K ALA* 3.8 6.7 - - + -
245K ARG 4.2 1.7 - - - +
246K MET* 3.8 6.1 + - - +
247K VAL 3.3 0.2 - - - -
248K ARG* 1.4 75.4 - - - +
250K VAL* 1.4 63.4 + - - +
251K PHE 3.5 0.6 + - - -
252K ARG* 3.7 12.1 + - - +
253K LEU* 3.9 10.4 + - - +
78L ARG* 3.1 33.2 + - - +
108M GLY* 3.8 5.2 + - - -
109M ALA 3.0 34.8 + - - +
110M ASN* 4.2 7.4 - - - +
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Residues in contact with VAL 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K ALA* 3.4 30.4 - - + +
148K ASP* 3.7 31.0 - - - +
149K SER 4.0 4.3 - - - +
154K LEU* 3.9 29.8 - - + -
156K SER* 5.9 0.4 - - - +
228K ILE* 6.1 1.8 - - + -
246K MET* 3.5 21.1 - - - +
247K VAL* 3.2 17.6 + - + +
249K ASP* 1.4 75.5 - - - +
251K PHE* 1.4 65.0 + - - +
252K ARG 3.5 0.3 + - - -
253K LEU* 3.8 4.7 + - - +
254K ALA* 3.7 15.1 + - + +
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Residues in contact with PHE 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K ASN* 5.9 1.3 - - - -
247K VAL* 3.5 5.5 + - + +
248K ARG 3.1 22.9 - - - -
250K VAL* 1.4 80.6 - - - +
252K ARG* 1.4 85.7 + - + +
253K LEU 3.3 0.2 - - - -
254K ALA* 3.3 16.9 + - - +
255K LYS* 3.3 43.3 + - + +
262K ILE* 5.6 3.2 - - + +
295K GLN* 3.3 31.2 - - + +
110M ASN* 3.7 10.5 - - - -
111M ILE* 3.1 37.9 - - + -
112M ASP* 2.9 25.6 - - - +
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Residues in contact with ARG 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K LYS* 5.8 6.5 - - - +
127K ASN* 4.1 29.0 + - + +
145K PRO* 4.0 18.1 - - + +
249K ASP 3.9 6.7 - - - +
250K VAL 3.4 0.4 - - - -
251K PHE* 1.4 103.5 - - + +
253K LEU* 1.3 65.0 + - - +
255K LYS* 3.1 40.8 + - - +
256K GLU* 3.2 55.1 + - - +
110M ASN* 3.7 18.2 - - - +
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Residues in contact with LEU 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K PRO* 5.4 2.5 - - + -
145K PRO* 3.6 23.5 - - - +
146K GLU* 3.9 36.6 - - + +
147K ALA 4.5 10.3 - - - +
148K ASP* 5.3 5.2 - - - +
249K ASP 3.9 3.6 + - - +
250K VAL 3.8 7.9 + - - +
251K PHE 3.3 0.6 - - - -
252K ARG* 1.3 78.0 - - - +
254K ALA* 1.3 64.0 + - - +
256K GLU* 3.2 32.2 + - - +
257K ASN* 2.9 45.5 + - - +
62L LYS* 5.2 9.9 - - - +
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Residues in contact with ALA 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K SER* 5.8 0.7 - - - +
228K ILE* 4.5 21.8 - - + -
250K VAL 3.7 7.2 + - - +
251K PHE* 3.3 15.8 + - - +
252K ARG 3.2 0.6 - - - -
253K LEU* 1.3 81.9 - - - +
255K LYS* 1.3 62.2 + - - +
257K ASN* 3.7 13.9 + - - +
258K ALA* 4.2 1.9 + - - -
260K ALA* 4.6 12.8 - - + +
262K ILE* 4.3 22.9 - - + -
305K VAL* 4.7 2.4 - - - +
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Residues in contact with LYS 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K ASN* 4.7 13.1 + - - +
251K PHE* 3.5 44.1 - - + +
252K ARG* 3.1 35.0 + - - +
254K ALA* 1.3 80.0 - - + +
256K GLU* 1.3 62.6 + - - +
258K ALA* 3.9 13.7 + - - +
262K ILE* 6.3 1.8 - - + -
295K GLN* 3.9 34.6 - - + +
298K GLY* 6.2 2.9 - - - -
299K PHE* 5.5 18.2 - - + -
305K VAL* 4.3 17.7 - - + +
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Residues in contact with GLU 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K PRO* 4.6 10.4 - - - +
145K PRO* 4.3 16.8 - - - +
252K ARG* 3.2 34.8 + - - +
253K LEU* 3.2 30.3 + - - +
255K LYS* 1.3 81.5 - - - +
257K ASN* 1.3 69.4 + - - +
258K ALA* 3.2 6.5 + - - +
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Residues in contact with ASN 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253K LEU* 2.9 44.0 + - - +
254K ALA* 4.2 5.9 - - - +
255K LYS 3.4 0.4 - - - -
256K GLU* 1.3 89.1 + - - +
258K ALA* 1.4 64.8 + - - +
259K PRO 3.9 6.2 - - - +
260K ALA* 5.7 0.5 - - - +
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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