Contacts of the strand formed by residues 216 - 221 (chain A) in PDB entry 1P5Q
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 HIS 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.2 3.3 - - - +
155A GLN* 2.7 39.5 + - + -
156A THR* 3.1 32.9 + - + +
214A GLY 3.1 18.5 + - - -
215A GLU* 1.3 73.4 - - - +
217A SER* 1.3 54.9 + - - +
247A LEU 3.8 3.4 - - - -
248A HIS* 3.2 52.3 - + + -
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Residues in contact with SER 217 (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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152A ARG* 3.5 11.9 + - - -
153A ARG 3.4 10.1 - - - -
154A ILE* 3.3 10.2 - - - -
155A GLN* 4.0 4.0 - - - -
211A MSE 4.4 4.5 - - - -
215A GLU* 2.5 30.5 + - - -
216A HIS* 1.3 76.4 + - - +
218A ILE* 1.3 69.0 + - - +
219A VAL* 4.9 1.1 - - - -
246A GLU* 3.6 5.2 - - - +
247A LEU* 3.1 44.1 + - - +
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Residues in contact with ILE 218 (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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151A ILE 3.9 0.3 - - - +
152A ARG* 3.1 6.2 - - - +
153A ARG* 2.8 39.8 + - + +
155A GLN* 3.9 22.4 - - + +
217A SER* 1.3 74.1 - - - +
219A VAL* 1.3 63.4 + - - +
220A TYR* 3.4 45.1 - - + +
244A LYS* 3.9 15.9 - - + +
245A TYR 3.2 3.4 - - - +
246A GLU* 3.7 35.2 - - + +
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Residues in contact with VAL 219 (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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150A ILE* 4.0 6.7 - - + -
151A ILE 3.5 3.8 - - - +
152A ARG* 4.1 11.2 - - + +
204A LEU* 5.2 2.0 - - + -
207A ALA* 3.8 29.6 - - + -
211A MSE 5.2 0.9 - - - -
217A SER* 4.9 2.9 - - - -
218A ILE* 1.3 80.2 - - - +
220A TYR* 1.3 65.0 + - - +
221A LEU* 3.6 31.6 + - + +
243A LEU 3.4 2.3 - - - +
244A LYS* 3.4 5.5 - - - -
245A TYR* 2.9 35.7 + - + +
247A LEU* 3.9 31.0 - - + -
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Residues in contact with TYR 220 (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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149A GLY 3.2 3.9 - - - +
150A ILE* 3.3 2.9 - - - -
151A ILE* 2.4 76.2 + - + +
153A ARG* 4.1 21.2 - - + +
218A ILE* 3.4 25.4 - - + +
219A VAL* 1.3 73.0 - - - +
221A LEU* 1.3 60.7 + - - +
222A LYS* 4.2 2.0 - - + -
243A LEU 3.5 3.1 - - - +
244A LYS* 3.3 44.1 - - + +
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Residues in contact with LEU 221 (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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149A GLY 3.3 4.5 - - - +
150A ILE* 3.6 22.2 - - + -
201A PRO* 4.1 19.3 - - + -
203A GLY* 3.4 33.7 - - - -
204A LEU* 3.7 5.4 - - + +
219A VAL* 3.6 13.5 - - + +
220A TYR* 1.3 73.8 - - - +
222A LYS* 1.3 69.5 - - - +
225A TYR* 4.3 3.6 - - + +
226A ALA* 4.4 6.9 - - + +
242A GLU* 3.3 3.5 - - - +
243A LEU* 2.8 47.7 + - + +
245A TYR* 3.8 34.8 - - + -
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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