Contacts of the strand formed by residues 245 - 250 (chain A) in PDB entry 3L49
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 ARG 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ASP* 5.4 4.9 - - + +
219A GLY 3.4 8.0 + - - +
220A ALA* 3.3 5.9 - - - -
221A ILE 3.0 22.7 + - - -
242A THR* 2.8 32.2 + - - +
243A ASP 4.4 2.2 + - - +
244A ILE* 1.3 82.4 + - - +
246A THR* 1.3 63.5 + - - +
247A TYR* 3.5 30.0 - - + +
262A PRO 5.2 5.3 + - - -
264A SER 4.4 5.7 + - - -
265A PRO* 3.2 37.2 - - - +
267A GLY* 4.1 12.6 - - - -
307A LYS* 3.9 19.7 - - - +
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Residues in contact with THR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ILE* 3.4 18.4 - - + -
229A MET* 4.0 12.3 - - - -
232A ALA* 4.1 14.4 - - + -
233A THR* 3.0 26.9 + - - +
236A LEU* 3.8 24.9 - - + -
245A ARG* 1.3 74.6 - - - +
247A TYR* 1.3 65.6 + - - +
255A PHE* 3.3 15.1 - - - -
265A PRO 3.0 6.9 + - - +
266A ALA* 3.5 5.9 - - - -
267A GLY* 2.8 31.2 + - - -
268A ALA 3.4 2.3 + - - -
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Residues in contact with TYR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 4.1 15.5 - - + -
143A GLN* 4.4 0.7 - - + -
144A MET* 3.5 60.6 + - + -
147A ASP* 2.7 42.0 + - - +
148A LEU* 6.0 0.4 - - + +
220A ALA* 4.2 4.9 - - + -
221A ILE 2.8 13.9 + - - +
222A TRP* 3.5 2.8 - - - -
223A ALA 3.2 23.7 + - - +
229A MET* 3.4 8.4 - - - +
245A ARG* 3.5 39.1 - - + +
246A THR* 1.3 74.3 - - - +
248A GLY* 1.3 58.2 + - - +
255A PHE* 4.7 0.7 - - - -
267A GLY* 3.8 13.0 - - - -
268A ALA* 3.5 26.9 - - + -
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Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.5 9.5 - - - +
223A ALA 3.6 12.3 - - - -
225A TRP 4.3 4.0 - - - -
226A ASP* 4.3 3.8 - - - -
229A MET* 4.2 9.9 - - - -
247A TYR* 1.3 74.6 - - - +
249A VAL* 1.3 62.9 + - - -
255A PHE* 4.2 3.2 - - - -
268A ALA 3.3 6.5 + - - -
269A VAL* 3.3 12.1 - - - -
270A ALA 3.2 18.7 + - - -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 3.9 21.5 - - + -
137A GLY* 6.1 0.2 - - - -
140A LEU* 3.8 17.5 - - + -
169A ARG* 3.6 38.1 - - + +
222A TRP* 6.1 0.4 - - + -
223A ALA 4.7 0.9 - - - +
224A CYS* 3.5 18.6 - - - +
225A TRP* 3.2 3.1 - - - +
226A ASP* 2.7 34.9 + - - +
248A GLY* 1.3 78.4 - - - +
250A ASP* 1.3 75.3 + - - +
270A ALA* 3.8 15.5 - - + +
272A GLN* 3.8 7.2 - - - +
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Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A UNL 2.8 36.2 - - - +
43A HIS* 4.4 4.0 + - - -
45A TRP* 3.7 25.1 - - + +
225A TRP* 4.1 8.0 - - - +
226A ASP* 3.3 12.7 + - + +
227A VAL* 5.8 0.7 - - - +
249A VAL* 1.3 79.4 - - - +
251A GLY* 1.3 60.7 + - - +
252A SER* 4.3 4.9 - - - +
269A VAL* 3.9 0.8 - - - +
270A ALA 2.8 16.9 + - - -
272A GLN* 2.6 61.8 + - - +
274A PRO* 5.1 0.7 - - - +
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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
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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