Contacts of the strand formed by residues 204 - 217 (chain F) in PDB entry 1C9T
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 LYS 204 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121F ILE* 4.2 1.1 - - - -
122F SER* 3.3 28.3 + - - +
123F LEU 3.3 21.6 + - - +
124F PRO* 4.0 22.4 - - + -
125F THR* 5.2 11.0 - - - +
200F VAL* 3.0 9.3 - - - -
201F CYS 2.9 32.4 + - - +
202F SER* 3.1 12.6 + - - +
203F GLY* 1.3 82.2 - - - +
209F LEU* 1.3 59.3 + - - +
210F GLN* 3.3 7.2 + - - +
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Residues in contact with LEU 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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45F SER* 3.7 24.7 - - - +
47F ILE* 4.5 1.1 - - + -
53F VAL* 3.3 32.8 - - + -
121F ILE* 3.9 16.3 - - + +
122F SER 2.8 18.5 + - - +
123F LEU* 4.3 15.9 - - + -
124F PRO* 3.2 22.9 - - + +
198F PRO* 3.7 21.3 - - + -
199F VAL 3.8 4.0 - - - +
200F VAL* 4.6 2.7 - - + +
204F LYS* 1.3 70.8 - - - +
210F GLN* 1.3 56.4 + - - +
211F GLY 4.0 8.7 - - - +
212F ILE* 5.4 2.7 - - + -
231F VAL* 3.4 22.9 - - + +
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Residues in contact with GLN 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F PRO* 3.3 22.8 - - - +
127F SER 3.4 10.7 - - - +
128F CYS* 4.0 7.5 - - - +
129F ALA* 3.5 30.8 + - + +
162F ILE* 5.0 0.2 - - + -
181F PHE* 3.3 18.3 - - + -
199F VAL 2.8 9.6 + - - +
201F CYS* 3.4 46.0 - - + +
204F LYS* 3.3 7.8 + - - +
209F LEU* 1.3 73.4 - - - +
211F GLY* 1.3 56.1 + - - +
230F LYS* 3.8 1.5 - - - +
231F VAL* 2.9 23.7 + - - -
232F CYS* 4.1 14.3 - - - +
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Residues in contact with GLY 211 (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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181F PHE* 3.5 15.0 - - - -
198F PRO* 3.7 2.6 - - - +
199F VAL* 2.9 34.9 + - - +
209F LEU* 3.7 4.6 - - - +
210F GLN* 1.3 82.2 - - - +
212F ILE* 1.3 66.5 + - - +
228F TYR* 4.4 0.2 - - - -
229F THR 3.0 12.1 - - - -
231F VAL* 3.7 2.7 - - - -
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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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53F VAL* 4.0 15.3 - - + -
54F SER* 3.6 21.5 - - - +
55F ALA* 3.7 11.9 - - + +
102F ASP 4.3 6.3 - - - +
103F ILE* 3.7 22.0 - - + -
196F GLY* 3.4 37.5 - - - +
197F GLY 3.4 3.4 - - - +
198F PRO* 6.0 0.2 - - + -
209F LEU* 5.4 2.7 - - + -
211F GLY* 1.3 74.3 - - - +
213F VAL* 1.3 71.5 + - - +
214F SER 3.1 1.9 + - - -
228F TYR* 3.2 5.7 - - - -
229F THR* 2.9 36.2 + - - +
231F VAL* 3.5 22.9 - - + -
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Residues in contact with VAL 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ALA* 4.0 3.8 - - - +
138F ILE* 3.9 19.3 - - + -
139F SER 5.0 1.3 - - - +
190F SER* 3.7 13.9 - - - +
194F ASP* 3.1 35.9 - - + +
195F SER* 3.5 4.7 - - - +
196F GLY 3.1 18.2 + - - -
197F GLY* 3.1 19.4 + - - +
198F PRO 4.6 2.0 - - - +
211F GLY 4.2 0.2 - - - -
212F ILE* 1.3 73.6 - - - +
214F SER* 1.3 58.5 + - - +
228F TYR* 3.3 22.8 - - + -
34L LYS* 3.4 31.0 - - + -
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Residues in contact with SER 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F HIS* 3.4 11.0 + - - -
99F LEU* 4.6 1.9 + - - +
102F ASP* 2.8 32.1 + - - +
195F SER* 3.5 1.4 + - - -
212F ILE 3.1 8.0 + - - -
213F VAL* 1.3 74.4 - - - +
215F TRP* 1.3 76.7 + - - +
227F VAL 3.2 15.5 + - - -
228F TYR* 4.3 4.3 - - - -
229F THR* 4.0 8.3 - - - -
33L CYS* 3.4 4.5 - - - -
34L LYS* 3.0 26.2 + - - +
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Residues in contact with TRP 215 (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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98F THR 4.7 5.4 - - - -
99F LEU* 3.6 28.8 - - + +
172F TYR* 3.8 20.0 - + - -
175F GLN* 4.0 26.9 - - + -
176F ILE* 4.0 14.1 - - + -
180F MET* 3.4 37.3 - - + +
214F SER* 1.3 99.1 - - - +
216F GLY* 1.3 72.6 + - - +
227F VAL* 2.8 46.1 + - + +
31L LEU* 3.2 37.5 - - + -
32L HIS 3.4 16.4 - - - +
33L CYS* 3.6 7.0 - - - +
34L LYS* 3.6 12.9 - - - +
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Residues in contact with GLY 216 (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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172F TYR* 3.9 12.1 - - - -
189F ASP* 6.0 0.4 - - - -
215F TRP* 1.3 93.8 - - - +
217F SER* 1.3 63.7 + - - -
219F GLY 3.6 6.3 + - - +
225F PRO 4.4 4.7 - - - -
226F GLY* 5.0 0.7 - - - -
227F VAL* 4.6 0.4 - - - -
31L LEU* 4.4 0.9 - - - -
32L HIS* 2.9 28.1 + - - +
34L LYS* 4.1 6.4 - - - +
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Residues in contact with SER 217 (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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172F TYR* 3.1 27.8 + - - -
189F ASP* 5.2 0.3 - - - +
216F GLY* 1.3 68.9 - - - -
219F GLY* 1.3 68.2 + - - +
220F CYS* 3.3 2.4 + - - -
221F GLN* 3.8 17.5 - - - +
224F LYS* 3.6 31.6 + - - +
30L ASP* 3.9 25.2 + - - -
31L LEU* 4.1 10.0 - - - +
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Residues in contact with GLY 219 (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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189F ASP* 4.5 1.6 - - - +
192F GLN* 4.5 11.2 - - - +
216F GLY* 3.6 6.6 + - - +
217F SER* 1.3 77.3 + - - +
220F CYS* 1.3 73.4 - - - -
221F GLN* 3.9 9.2 - - - -
30L ASP* 3.2 22.6 + - - +
32L HIS* 5.0 1.0 - - - +
34L LYS* 4.3 6.4 + - - -
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Residues in contact with CYS 220 (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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17F VAL* 3.5 15.5 - - + -
146F SER* 4.0 18.6 + - - +
189F ASP* 3.9 4.7 - - - -
190F SER 3.6 3.6 - - - +
191F CYS* 2.0 57.0 - - + -
192F GLN* 3.6 11.7 - - - -
217F SER 3.3 0.4 + - - -
219F GLY* 1.3 84.1 - - - -
221F GLN* 1.3 92.2 + - - +
34L LYS* 4.3 0.7 - - - -
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Residues in contact with ALA 221 (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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17F VAL* 3.5 27.4 - - + -
146F SER* 4.8 4.5 - - - -
187F GLY* 3.2 4.6 - - - -
188F GLY* 3.0 43.6 + - - +
189F ASP* 3.1 30.2 + - + +
220F CYS* 1.3 72.5 - - - +
221F GLN* 1.3 64.6 + - - +
222F LYS 3.5 1.2 + - - -
224F LYS 4.8 0.7 - - - -
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Residues in contact with GLN 221 (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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146F SER* 4.8 12.9 - - - -
147F SER* 5.5 2.1 + - - -
184F TYR 5.1 1.6 - - - +
187F GLY* 4.5 2.6 - - - -
217F SER* 3.8 17.7 + - - +
219F GLY* 3.9 7.2 - - - -
220F CYS 2.9 36.8 + - - -
221F ALA* 1.3 79.6 - - - +
222F LYS* 1.3 69.0 + - - +
223F ASN 3.5 0.5 + - - -
224F LYS* 3.0 34.3 + - + +
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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