Contacts of the strand formed by residues 210 - 217 (chain A) in PDB entry 4IYT
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 PHE 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LYS* 3.4 4.4 - - - +
50A MET* 2.7 45.6 + - + +
80A ILE* 3.7 19.1 - - + -
95A LEU 3.6 2.7 - - - -
96A PRO* 3.4 22.4 - - + -
135A ILE* 3.7 1.1 - - - +
137A TYR* 3.6 31.0 - + - -
144A SER* 5.0 0.2 - - - -
156A TRP* 3.5 47.1 - + + -
158A ILE* 3.6 21.8 - - + -
206A PHE* 3.7 21.3 - + - -
208A PRO* 3.7 9.6 - - + -
209A SER* 1.4 88.5 - - - +
211A ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 211 (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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47A ILE* 4.2 6.3 - - + -
48A LEU 3.3 8.3 - - - +
49A LYS* 4.0 12.6 - - + -
50A MET* 4.0 2.7 - - - -
93A ASN* 4.5 4.3 - - - +
94A TYR* 3.0 5.9 - - - +
95A LEU* 2.8 47.5 + - + +
109A LEU* 3.9 33.2 - - + +
133A LYS* 3.5 46.2 - - + +
134A THR 4.0 2.9 - - - +
135A ILE* 3.4 26.0 - - + +
156A TRP* 3.8 2.1 - - - -
210A PHE* 1.3 75.7 - - - +
212A ALA* 1.3 66.7 + - - +
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Residues in contact with ALA 212 (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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47A ILE* 3.7 1.2 - - - +
48A LEU* 2.8 36.8 + - - +
50A MET* 3.8 9.4 - - + +
82A LEU* 3.4 32.3 - - + -
91A LEU* 3.7 14.1 - - + -
93A ASN 3.5 5.8 - - - +
94A TYR* 4.3 5.4 - - + -
154A VAL* 4.4 3.8 - - + -
211A ILE* 1.3 77.9 - - - +
213A THR* 1.3 62.3 + - - +
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Residues in contact with THR 213 (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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45A ALA* 5.0 0.4 - - + -
46A LEU 3.3 13.9 - - - +
47A ILE* 3.8 4.3 - - + +
91A LEU* 3.5 7.1 - - - +
92A ILE* 2.9 39.0 + - + -
93A ASN* 2.8 35.6 + - - +
109A LEU* 3.2 20.6 - - - +
117A PHE* 3.5 32.1 - - + -
212A ALA* 1.3 73.9 + - - +
214A VAL* 1.3 69.7 + - - +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 3.2 5.4 - - - +
46A LEU* 2.8 53.6 + - + +
48A LEU* 4.0 12.8 - - + -
82A LEU* 4.9 3.6 - - + -
84A THR* 5.6 1.8 - - + -
89A VAL* 3.7 17.0 - - + -
90A ASP 3.2 6.1 - - - +
91A LEU* 3.9 25.4 - - + +
92A ILE* 4.5 1.1 - - - -
212A ALA 4.2 0.2 - - - -
213A THR* 1.3 82.0 - - - +
215A SER* 1.3 59.2 - - - +
226A PHE* 3.7 33.7 - - + -
273A TRP* 4.1 6.7 - - + -
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Residues in contact with SER 215 (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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41A TYR* 3.9 20.6 - - - -
43A LYS* 4.1 18.9 + - - +
44A ASP 3.2 9.0 - - - -
45A ALA* 4.3 0.2 - - - +
88A ASN 4.5 0.2 - - - -
89A VAL* 3.2 9.4 - - - +
90A ASP* 2.8 52.7 + - - +
92A ILE* 3.6 14.8 - - - +
214A VAL* 1.3 75.1 - - - +
216A HIS* 1.3 61.5 + - - +
217A GLU* 5.0 1.1 + - - -
273A TRP* 5.1 0.7 - - - -
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Residues in contact with HIS 216 (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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43A LYS* 3.7 5.4 - - - +
44A ASP* 2.7 63.9 + - + +
86A ASP* 4.0 2.6 + - - -
88A ASN* 3.3 23.1 + - + +
89A VAL* 3.9 4.3 - - + -
215A SER* 1.3 76.1 - - - +
217A GLU* 1.3 79.7 + - - +
218A LYS 3.3 0.5 + - - -
219A GLY 4.8 2.0 - - - -
220A SER* 3.2 13.7 + - - -
221A GLY* 2.9 31.4 + - - -
223A THR 5.1 0.2 + - - -
224A SER* 3.8 10.8 + - - -
273A TRP* 3.5 44.3 - + + -
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Residues in contact with GLU 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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43A LYS* 3.1 40.0 + - - +
88A ASN* 3.2 28.4 + - - +
90A ASP* 4.0 12.3 - - - +
215A SER* 5.0 1.4 + - - -
216A HIS* 1.3 78.4 - - - +
218A LYS* 1.3 65.5 + - - +
220A SER* 2.7 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