Contacts of the strand formed by residues 204 - 215 (chain D) in PDB entry 3L3T
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 204 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D ILE* 4.4 1.8 - - - -
122D SER* 3.4 11.8 + - - +
123D LEU 3.8 8.0 + - - +
124D PRO* 3.3 10.6 - - + +
125D THR* 3.2 52.0 + - - +
127D ALA 4.5 0.9 + - - -
200D VAL* 3.3 8.0 - - - +
201D CYS 3.0 29.9 + - - +
202D ASN 3.2 9.3 + - - +
203D GLY* 1.3 85.1 - - - +
209D LEU* 1.3 59.2 + - - +
210D GLN* 3.2 20.4 + - - +
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER* 3.7 35.7 - - - +
47D ILE* 4.0 17.7 - - + -
53D VAL* 4.3 17.9 - - + -
121D ILE* 4.1 14.1 - - + +
122D SER 2.8 17.9 + - - +
123D LEU* 5.1 3.6 - - + -
124D PRO* 2.9 22.9 - - - +
198D PRO* 3.8 6.1 - - + -
199D VAL 3.8 15.5 - - - +
200D VAL* 4.3 4.9 - - + -
204D GLN* 1.3 70.4 - - - +
210D GLN* 1.3 58.3 + - - +
211D GLY 3.6 23.3 - - - +
212D VAL* 5.4 0.4 - - + -
231D VAL* 3.4 19.4 - - + +
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Residues in contact with GLN 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D PRO* 3.6 12.6 - - - +
127D ALA 3.1 23.2 + - - +
128D PRO* 4.3 1.8 + - - +
129D PRO* 3.4 40.0 - - + +
181D PHE* 3.7 13.2 - - + -
199D VAL* 3.0 11.2 + - + +
201D CYS* 3.7 36.7 + - + +
204D GLN* 3.2 24.9 + - - +
209D LEU* 1.3 74.3 - - - +
211D GLY* 1.3 58.8 + - - +
229D THR 3.6 1.2 - - - +
230D LYS* 3.8 0.9 - - - -
231D VAL* 3.0 23.1 + - - +
232D TYR* 4.5 3.3 - - - +
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Residues in contact with GLY 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D PHE* 4.0 9.0 - - - -
197D GLY 3.8 1.4 - - - +
199D VAL* 3.1 40.2 + - - +
209D LEU* 3.5 11.5 - - - +
210D GLN* 1.3 80.7 - - - +
212D VAL* 1.3 66.9 + - - +
228D TYR* 4.6 0.4 - - - -
229D THR 3.1 9.6 - - - -
231D VAL* 3.9 2.4 - - - +
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Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D VAL* 3.9 18.4 - - + -
54D SER* 3.6 18.4 - - - +
55D ALA* 3.7 5.4 - - + +
102D ASP 4.7 0.9 - - - +
103D ILE* 4.3 7.6 - - + -
196D GLY* 3.6 31.0 - - - +
197D GLY 3.5 2.9 - - - +
209D LEU* 5.4 0.9 - - + -
211D GLY* 1.3 77.5 - - - +
213D VAL* 1.3 71.3 + - - +
214D SER* 3.1 3.0 + - - -
228D TYR* 3.2 7.3 - - - +
229D THR* 3.0 42.7 + - - +
231D VAL* 3.6 20.4 - - + -
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Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 4.0 3.5 - - - +
138D ILE* 4.2 17.0 - - + -
139D SER 5.0 1.6 - - - +
190D SER* 3.7 22.9 - - - +
194D ASP* 3.3 35.2 - - + +
195D ALA* 3.6 12.7 - - - +
196D GLY* 2.9 23.2 + - - +
197D GLY* 3.1 21.2 + - - +
198D PRO 4.7 1.8 - - - +
211D GLY 4.2 0.2 - - - -
212D VAL* 1.3 71.9 - - - +
214D SER* 1.3 61.9 + - - +
228D TYR* 3.4 19.9 - - + -
15H LYS* 3.9 14.4 - - + -
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Residues in contact with SER 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D HIS* 3.1 20.9 - - - -
99D LEU* 4.9 1.4 + - - +
102D ASP* 2.7 33.1 + - - +
180D MET* 6.1 1.0 - - - +
212D VAL* 3.1 8.8 + - - -
213D VAL* 1.3 75.6 - - - +
215D TRP* 1.3 80.0 + - - +
227D VAL* 3.3 17.0 + - - -
228D TYR* 4.2 2.2 - - - -
229D THR* 4.1 10.5 - - - -
14H CYS* 3.6 0.3 - - - -
15H LYS* 3.4 17.1 + - - +
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Residues in contact with TRP 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D THR 5.6 0.9 - - - -
99D LEU* 3.7 28.2 - - + +
172D TYR* 3.5 43.3 - + - -
175D LYS* 4.0 35.9 - - + -
176D ILE* 4.1 5.4 - - + -
180D MET* 3.6 28.2 - - + +
214D SER* 1.3 98.8 - - - +
216D GLY* 1.3 77.8 + - - +
217D HIS* 4.7 1.1 - - + -
226D GLY 3.7 0.5 - - - -
227D VAL* 2.7 60.5 + - + +
13H PRO* 3.4 32.5 - - + +
14H CYS* 4.0 2.7 - - - -
15H LYS* 3.8 13.8 + - - +
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Residues in contact with GLY 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D TYR* 3.5 11.7 - - - -
189D ASP* 6.1 0.2 - - - -
215D TRP* 1.3 93.7 - - - +
217D HIS* 1.3 61.9 + - - -
219D GLY 3.3 12.2 + - - +
224D ARG 5.5 0.7 - - - -
225D PRO 4.7 1.6 - - - -
226D GLY* 4.9 0.4 - - - -
227D VAL 4.7 1.8 - - - -
13H PRO* 3.3 24.9 + - - +
15H LYS* 4.1 8.4 - - - +
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Residues in contact with HIS 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D TYR* 3.1 19.4 + - + -
215D TRP* 5.5 0.7 - - + -
216D GLY* 1.3 69.8 - - - -
219D GLY* 1.3 63.7 + - - +
221D TRP* 3.7 38.0 - - - +
224D ARG* 3.3 57.2 + - + +
13H PRO* 5.7 0.7 - - - -
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Residues in contact with GLY 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ASP* 4.8 1.8 - - - +
192D GLN* 5.7 2.2 + - - -
216D GLY* 3.3 14.7 + - - +
217D HIS* 1.3 79.0 + - - +
220D CYS* 1.3 69.5 + - - -
221D TRP* 4.1 19.5 - - - -
224D ARG 5.3 0.5 - - - +
13H PRO* 5.8 0.8 - - - +
15H LYS* 4.2 8.1 + - - -
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Residues in contact with CYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 4.2 8.5 - - + -
145D LEU 4.8 0.2 - - - +
146D SER* 2.6 39.2 + - - +
189D ASP* 4.2 3.8 - - + -
190D SER 3.9 5.8 - - - +
191D CYS* 2.0 60.1 - - + -
192D GLN* 3.4 14.1 - - - -
219D GLY* 1.3 79.2 - - - -
221D TRP* 1.3 69.9 + - - +
15H LYS* 4.6 2.7 - - - -
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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