Contacts of the strand formed by residues 207 - 216 (chain F) in PDB entry 3SDI
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 ASP 207 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.8 2.8 - - - +
54F ILE* 2.8 49.4 + - + +
202F HIS* 4.5 1.1 - - - -
206F LYS* 1.3 77.0 + - - +
208F PHE* 1.3 87.6 + - - +
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Residues in contact with PHE 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F GLU* 4.1 18.2 - - + -
52F LYS 3.2 17.0 - - - +
53F LEU* 4.5 1.8 - - - -
54F ILE* 3.8 10.4 - - - +
197F ILE* 3.8 24.5 - - + -
198F TYR* 3.6 55.5 + + - -
202F HIS* 3.4 42.0 - + + +
207F ASP* 1.3 97.9 + - - +
209F GLU* 1.3 71.2 + - - +
210F LEU* 4.6 6.7 - - + -
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Residues in contact with GLU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F GLU* 3.9 0.5 - - - -
52F LYS* 2.8 66.8 + - + +
54F ILE* 3.9 18.7 - - + +
60F VAL 4.6 1.4 - - - +
61F PRO* 3.4 13.2 - - - +
62F GLN* 2.8 58.5 + - - +
208F PHE* 1.3 80.1 - - - +
210F LEU* 1.3 68.2 + - - +
211F GLU* 5.1 0.2 - - - +
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Residues in contact with LEU 210 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49F ALA* 4.7 0.7 - - + -
50F VAL 3.9 5.8 - - - +
52F LYS* 5.0 0.4 - - - -
62F GLN* 5.1 3.5 + - - +
194F ALA* 3.9 18.2 - - + +
197F ILE* 3.8 36.3 - - + -
198F TYR* 4.3 11.2 - - + +
208F PHE* 4.6 10.3 - - + -
209F GLU* 1.3 83.3 - - - +
211F GLU* 1.3 66.4 + - - +
212F ILE* 3.7 36.2 + - + -
229F LEU* 4.5 18.7 - - + +
233F ILE* 3.8 32.9 - - + +
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Residues in contact with GLU 211 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49F ALA* 3.2 5.0 - - - +
50F VAL* 3.0 46.8 + - + +
52F LYS* 3.3 35.4 + - + -
62F GLN* 5.3 1.0 - - - +
65F VAL* 3.4 22.1 - - - +
66F LYS* 2.7 29.5 + - - +
67F ILE* 3.0 25.7 + - + +
209F GLU* 4.1 0.8 + - - +
210F LEU* 1.3 74.2 - - - +
212F ILE* 1.3 65.6 + - - +
223F PHE* 4.5 10.1 - - + -
229F LEU* 5.4 0.7 - - - -
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Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL* 3.8 21.3 - - + -
48F PHE 3.2 12.1 - - - +
49F ALA* 4.3 6.3 - - + -
67F ILE* 3.9 3.1 - - - -
190F VAL* 4.1 21.5 - - + +
193F ALA* 4.9 1.1 - - + -
194F ALA* 4.0 19.5 - - + +
210F LEU* 3.7 32.7 - - + -
211F GLU* 1.3 81.3 - - - +
213F SER* 1.3 65.7 + - - +
223F PHE* 4.0 6.9 - - - -
224F VAL* 3.0 44.9 + - + +
229F LEU* 4.0 15.8 - - + +
232F ALA* 4.5 4.0 - - + -
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Residues in contact with SER 213 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F VAL* 3.6 4.0 - - - +
48F PHE* 2.9 35.9 + - - +
67F ILE* 3.2 24.0 - - - +
212F ILE* 1.3 76.6 - - - +
214F TRP* 1.3 64.5 + - - +
221F HIS* 2.8 32.9 + - - -
222F LYS 3.5 12.6 - - - -
223F PHE* 4.0 8.3 - - - -
224F VAL* 3.9 5.2 - - - -
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Residues in contact with TRP 214 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46F VAL 3.3 12.6 - - - +
47F VAL* 4.4 8.1 - - + -
48F PHE* 5.0 1.6 - - - +
186F ALA* 4.0 25.8 - - + -
187F ARG* 4.4 6.7 - - + -
190F VAL* 3.6 21.5 - - + -
213F SER* 1.3 77.3 + - - +
215F CYS* 1.3 62.0 + - - +
216F SER* 4.1 3.1 - - - -
218F THR* 3.6 70.2 + - + +
220F LEU 3.6 1.7 - - - +
221F HIS* 3.6 5.6 - - - -
222F LYS* 2.9 51.7 + - - +
223F PHE 4.5 4.4 + - - -
224F VAL* 3.7 18.3 - - + +
228F LEU* 3.6 29.4 - - + -
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Residues in contact with CYS 215 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F GLY* 3.1 5.2 - - - -
46F VAL* 3.0 43.5 + - + +
73F HIS 3.4 23.6 - - - +
139F GLY 5.2 0.9 - - - +
140F GLY* 4.3 2.5 - - - -
141F VAL* 3.7 19.8 - - - +
214F TRP* 1.3 75.3 - - - +
216F SER* 1.3 59.4 + - - +
219F GLY 3.6 24.9 - - - -
220F LEU 3.5 15.9 - - - +
221F HIS* 4.2 10.5 - - + -
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Residues in contact with SER 216 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F CYS* 5.2 0.2 - - - -
44F ASP* 2.8 31.5 + - - -
45F GLY* 4.0 2.5 - - - -
46F VAL 5.4 0.2 - - - -
186F ALA* 3.7 17.5 - - - +
214F TRP* 4.1 6.4 - - - -
215F CYS* 1.3 75.4 - - - +
217F LEU* 1.3 63.0 + - - +
218F THR* 2.8 61.0 + - - +
219F GLY* 2.9 12.1 + - - -
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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