Contacts of the strand formed by residues 225 - 236 (chain A) in PDB entry 5ZF6
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 GLN 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLY* 3.2 6.1 - - - -
221A ALA* 2.6 38.6 + - + -
222A PRO 3.3 19.3 - - - +
223A LYS* 3.6 15.1 - - + +
224A SER* 1.3 82.0 - - - +
226A ILE* 1.3 60.6 + - - +
249A VAL* 5.6 0.4 - - - -
522A GLY 5.6 3.6 + - - -
523A GLU* 5.9 3.8 + - - +
524A ILE* 5.0 6.9 - - - +
564A PRO 4.5 2.8 + - - +
565A GLY* 3.6 31.9 + - - -
566A ILE 3.5 5.2 - - - -
567A PRO* 3.2 39.1 - - - +
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Residues in contact with ILE 226 (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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218A VAL* 4.4 3.1 - - + -
219A ALA 3.8 5.8 - - - +
220A GLY* 4.7 0.2 - - - -
224A SER 4.9 0.2 - - - +
225A GLN* 1.3 73.0 - - - +
227A VAL* 1.3 61.9 + - - +
228A MET 4.0 10.8 - - - +
229A LEU* 3.6 28.7 - - + -
245A ILE* 3.9 19.7 - - + -
249A VAL* 3.7 31.9 - - + -
561A ILE* 3.6 19.0 - - + +
565A GLY* 3.1 2.6 - - - -
566A ILE 2.9 35.5 + - - +
568A ILE* 4.3 14.8 - - + -
571A VAL* 3.7 26.2 - - + -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 3.9 12.2 - - - +
137A SER* 3.8 21.8 - - - +
140A PRO* 4.9 7.2 - - + -
141A LEU* 4.1 12.3 - - + -
188A VAL* 4.6 5.2 - - + -
219A ALA* 3.0 29.7 + - + +
220A GLY 4.4 0.9 - - - +
221A ALA* 3.7 22.9 - - + -
226A ILE* 1.3 76.6 - - - +
228A MET* 1.3 63.9 + - - +
559A ALA 4.7 0.2 - - - +
561A ILE* 3.5 31.3 + - - +
563A LEU 4.9 0.2 - - - +
564A PRO* 4.0 3.6 - - + -
565A GLY* 3.7 23.3 - - - +
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Residues in contact with MET 228 (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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133A ILE* 3.8 19.7 - - + +
136A ARG* 3.7 35.9 - - + +
137A SER* 3.5 33.9 - - - +
170A ILE* 4.6 2.0 - - + -
217A VAL* 3.6 28.7 - - + +
218A VAL* 3.4 6.3 - - - -
219A ALA* 3.0 41.6 + - + +
226A ILE* 3.8 2.3 - - - +
227A VAL* 1.3 83.2 - - - +
229A LEU* 1.3 67.4 + - - +
230A GLU* 3.8 16.4 - - - -
559A ALA 4.5 3.6 - - - -
561A ILE* 5.0 0.2 - - - -
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Residues in contact with LEU 229 (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 ARG* 3.4 3.9 + - - -
216A LEU* 3.7 27.8 - - + -
217A VAL 3.6 0.7 - - - +
218A VAL* 3.9 23.8 - - + -
226A ILE* 3.6 25.4 - - + -
228A MET* 1.3 72.4 - - - +
230A GLU* 1.3 59.3 + - - +
245A ILE* 4.2 18.8 - - + -
545A PHE* 4.4 4.7 - - + -
557A LEU* 3.9 14.5 - - + +
558A GLN* 3.4 2.8 + - - -
559A ALA* 2.7 49.6 + - + +
571A VAL* 3.7 33.2 - - + -
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Residues in contact with GLU 230 (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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132A ARG* 3.6 9.4 + - - +
133A ILE* 4.1 18.5 - - + +
136A ARG* 3.2 32.1 - - - +
215A ASN 3.7 1.3 - - - +
216A LEU* 3.7 0.6 - - - +
217A VAL* 2.8 40.2 + - + +
228A MET* 3.8 9.8 - - - -
229A LEU* 1.3 73.5 - - - +
231A ALA* 1.3 65.5 + - - +
453A LEU* 4.4 1.7 - - - +
456A LYS* 2.3 34.7 + - - -
557A LEU 3.5 2.7 - - - -
558A GLN* 2.9 31.9 - - + +
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Residues in contact with ALA 231 (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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214A LEU* 4.3 1.1 - - + -
215A ASN 3.2 8.5 - - - +
216A LEU* 3.5 24.0 - - + -
230A GLU* 1.3 78.1 + - - +
232A SER* 1.3 58.4 + - - +
241A PHE* 3.6 29.8 - - + -
456A LYS* 3.7 12.3 - - - -
556A ALA* 3.3 2.4 - - - -
557A LEU* 2.7 40.0 + - + +
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Residues in contact with SER 232 (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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214A LEU* 3.6 2.5 - - - +
215A ASN* 2.8 45.1 + - - +
231A ALA* 1.3 73.8 - - - +
233A ALA* 1.3 61.9 + - - +
456A LYS* 3.6 33.4 - - - +
460A PRO* 6.5 0.2 - - - -
555A THR 3.4 9.0 - - - -
556A ALA* 4.2 0.2 - - - +
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Residues in contact with ALA 233 (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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213A THR 3.5 7.9 - - - +
214A LEU* 3.8 19.1 - - + -
232A SER* 1.3 77.0 - - - +
234A GLU* 1.3 60.3 + - - +
235A ASN 2.9 9.3 + - - -
236A ILE* 3.9 14.1 - - + -
241A PHE* 4.4 6.5 - - + -
460A PRO* 3.1 14.0 - - - +
554A ILE 3.2 20.9 - - - +
555A THR* 2.7 23.3 + - - +
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Residues in contact with GLU 234 (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 SER 4.6 4.9 - - - +
213A THR* 2.9 41.6 + - + +
233A ALA* 1.3 68.3 - - - +
235A ASN* 1.3 70.5 + - - +
236A ILE* 3.2 4.5 + - - +
421A LYS* 4.2 5.7 + - - -
459A TYR* 3.6 27.2 - - - -
460A PRO* 3.3 31.2 - - - +
464A ARG* 5.1 8.0 + - - -
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Residues in contact with ASN 235 (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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233A ALA 2.9 12.5 + - - -
234A GLU* 1.3 73.6 - - - +
236A ILE* 1.3 67.8 + - - +
237A LEU* 5.7 0.3 - - - +
460A PRO* 4.2 5.5 - - + +
461A VAL* 5.2 5.1 - - + +
503A SER* 5.8 0.6 + - - -
504A SER* 5.5 3.4 - - - -
550A THR* 2.6 44.6 + - - +
552A LYS* 4.5 6.7 - - - +
553A GLY* 3.2 23.4 - - - +
554A ILE 3.3 10.1 - - - -
555A THR* 4.0 7.9 - - + +
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Residues in contact with ILE 236 (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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195A ILE* 4.0 20.9 - - + -
213A THR* 3.1 42.0 - - - +
214A LEU* 4.0 11.9 - - + -
233A ALA* 3.9 7.9 - - + -
234A GLU 3.9 8.1 - - - +
235A ASN* 1.3 79.0 - - - +
237A LEU* 1.3 70.3 + - - +
240A ASP* 4.3 5.2 - - + +
241A PHE* 3.8 41.7 - - + +
553A GLY* 3.1 1.7 - - - -
554A ILE* 2.9 26.4 + - + +
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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