Contacts of the strand formed by residues 217 - 222 (chain A) in PDB entry 4F5G
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 LEU 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.0 12.1 - - + -
130A VAL* 4.7 0.4 - - + -
182A GLY* 4.8 2.4 - - - +
183A ASP 2.9 14.9 + - - +
184A VAL* 3.1 18.4 - - + +
185A VAL 3.0 21.2 + - - -
215A GLY 3.8 1.2 + - - -
216A TRP* 1.3 70.3 - - - +
218A PRO* 1.3 74.3 - - + +
247A GLU* 3.8 41.5 - - + +
248A LEU* 4.1 4.5 - - - +
249A ILE* 3.9 16.6 - - + -
11B THR* 4.1 21.3 - - + +
12B PHE* 3.8 29.6 - - + -
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Residues in contact with PRO 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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185A VAL* 3.4 9.6 - - + +
187A PHE* 5.1 1.6 - - + -
211A SER* 3.5 8.1 - - - +
216A TRP* 3.3 8.7 - - + +
217A LEU* 1.3 87.3 - - + +
219A LEU* 1.3 60.4 + - - +
220A ILE* 4.0 7.0 - - + -
241A PHE* 3.6 26.7 - - + -
245A HIS* 3.4 28.9 - - + +
247A GLU 3.6 18.6 - - - +
248A LEU* 3.6 12.5 - - + +
249A ILE 3.1 22.0 + - - +
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Residues in contact with LEU 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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117A LEU* 3.9 22.0 - - + -
120A ALA* 4.3 11.7 - - + -
124A LEU* 5.0 3.1 - - + -
147A PHE* 4.1 27.4 - - + -
184A VAL* 3.6 22.9 - - + -
185A VAL 2.9 7.6 + - - +
186A LEU* 3.2 12.2 - - + -
187A PHE 3.0 24.9 + - - +
217A LEU 3.5 0.6 + - - -
218A PRO* 1.3 75.0 - - - +
220A ILE* 1.3 78.4 + - - +
221A ASP 3.7 2.4 + - - +
249A ILE* 3.3 33.4 - - + +
251A ALA* 4.3 6.3 - - + -
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Residues in contact with ILE 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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187A PHE* 3.4 24.5 - - + -
189A GLY* 3.7 27.4 - - - +
204A TRP* 4.9 3.8 - - + -
218A PRO* 4.7 7.0 - - + -
219A LEU* 1.3 79.2 - - - +
221A ASP* 1.3 63.4 + - - +
222A ILE* 4.2 8.5 - - + -
238A LEU* 4.3 31.2 - - + -
241A PHE* 4.3 28.7 - - + -
248A LEU* 5.1 5.2 - - + -
249A ILE 2.9 11.6 + - - +
250A VAL* 3.4 13.7 - - + +
251A ALA 2.9 26.3 + - - +
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Residues in contact with ASP 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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113A GLY* 5.9 0.7 - - - -
117A LEU* 3.7 8.3 - - + +
143A HIS* 2.6 24.1 + - - +
186A LEU* 3.9 23.3 - - + -
187A PHE 2.9 6.8 + - - +
188A HIS* 3.3 8.5 - - + +
189A GLY 2.9 22.1 + - - -
190A CYS 5.5 0.3 - - - +
219A LEU* 3.7 7.0 + - + -
220A ILE* 1.3 71.2 - - - +
222A ILE* 1.3 65.5 + - - +
223A ALA* 4.1 1.2 + - - +
251A ALA* 3.5 8.1 - - - +
256A LLP 2.5 46.4 + - - +
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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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92A LEU* 3.7 23.6 - - + -
189A GLY* 4.2 19.1 - - - +
190A CYS* 4.3 7.4 - - - +
220A ILE* 4.2 2.7 - - + -
221A ASP* 1.3 74.7 + - - +
223A ALA* 1.3 60.8 + - - +
225A GLN* 3.8 42.3 - - + +
234A ASP 4.0 20.6 - - - +
235A ALA* 4.8 2.5 - - - -
238A LEU* 4.4 15.3 - - + -
250A VAL* 3.8 16.6 - - + -
251A ALA 2.9 13.0 + - - +
252A SER* 3.2 5.1 - - - -
253A SER 3.1 20.8 + - - +
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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