Contacts of the strand formed by residues 220 - 225 (chain A) in PDB entry 4UC5
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 SER 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A SER 3.6 5.8 - - - -
214A VAL* 4.3 0.8 - - - +
218A GLY 4.0 0.4 + - - -
219A HIS* 1.3 81.8 + - - +
221A ALA* 1.3 59.4 + - - +
17B GLU* 3.5 1.2 - - - -
18B LEU* 3.0 38.6 + - - +
19B LEU 4.2 0.7 + - - -
20B PRO* 4.2 0.5 - - - +
150B ILE* 5.1 6.1 - - - -
154B TYR* 3.7 19.8 + - - -
214B VAL* 4.0 22.0 - - - -
218B GLY* 2.8 26.9 + - - -
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Residues in contact with ALA 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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212A LEU* 3.3 8.1 - - - +
213A SER 2.5 40.1 + - - +
215A THR* 3.6 20.4 - - + +
219A HIS 3.6 7.2 - - - +
220A SER* 1.3 76.2 - - - +
222A ILE* 1.3 60.9 + - - +
223A VAL* 4.1 1.1 - - + -
15B VAL* 3.8 14.8 - - + -
16B LYS 3.2 13.9 - - - +
18B LEU* 3.7 10.3 - - - +
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Residues in contact with ILE 222 (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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210A HIS* 3.7 42.2 - - + -
211A PHE 3.8 4.3 - - - +
212A LEU* 3.7 22.4 - - + -
221A ALA* 1.3 74.4 - - - +
223A VAL* 1.3 62.3 + - - +
224A HIS* 4.1 0.4 + - + -
14B GLU 3.9 1.2 - - - +
15B VAL* 3.5 3.3 - - - -
16B LYS* 2.9 60.2 + - + +
18B LEU* 3.4 25.5 - - + +
111B ASN* 4.9 5.8 - - + +
119B PHE* 5.8 3.1 - - + +
121B ILE* 3.9 21.1 - - + -
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Residues in contact with VAL 223 (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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153A GLN* 5.9 1.8 - - - +
209A HIS 3.6 1.0 - - - +
210A HIS* 3.1 7.7 - - - -
211A PHE* 2.9 60.3 + - + +
213A SER* 3.6 27.1 - - - +
214A VAL 5.5 0.9 - - - +
221A ALA 4.7 1.1 - - - +
222A ILE* 1.3 78.3 - - - +
224A HIS* 1.3 60.8 + - - +
225A THR* 4.0 2.8 + - + -
12B ILE* 3.7 30.5 - - + -
14B GLU 3.7 2.9 - - - -
15B VAL* 4.3 23.6 - - + +
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Residues in contact with HIS 224 (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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208A SER* 2.9 28.3 + - - -
209A HIS 3.5 3.4 - - - -
210A HIS* 3.3 40.6 + + + +
222A ILE* 4.1 1.0 + - + -
223A VAL* 1.3 71.8 - - - +
225A THR* 1.3 57.4 + - - +
12B ILE* 3.7 3.1 - - - +
13B LYS* 2.7 56.8 + - + +
14B GLU* 2.9 33.9 + - + +
16B LYS* 6.5 0.9 - - + -
119B PHE* 5.9 1.6 - + - -
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Residues in contact with THR 225 (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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176A GLU 3.9 0.2 - - - +
179A SER* 2.8 37.1 + - - +
180A GLY* 3.4 23.1 - - - +
208A SER* 2.4 32.7 + - - -
209A HIS 2.9 29.6 + - - +
211A PHE* 3.8 24.5 - - + -
223A VAL* 4.3 0.9 - - + -
224A HIS* 1.3 78.7 - - - +
226A GLY* 1.3 55.9 + - - +
11B LYS 3.6 4.7 - - - -
12B ILE* 4.1 6.3 - - + +
13B LYS* 3.4 4.1 - - - -
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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