Contacts of the strand formed by residues 207 - 215 (chain D) in PDB entry 1RD3
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 TRP 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C GLY* 2.9 24.6 + - - +
4C ARG* 3.2 31.8 - - - +
8C GLU* 2.7 25.5 + - - -
14C ASP* 3.4 43.1 - - + -
29D TRP* 3.3 34.8 - + + -
121D VAL* 3.3 4.3 - - + +
122D CYS* 3.2 24.9 + - - +
137D ARG* 3.2 24.5 - - - -
200D VAL* 3.5 30.7 - - + -
201D MET 3.5 3.6 - - - -
202D LYS* 3.8 34.7 - - + +
206D ARG* 1.3 72.4 - - - +
208D TYR* 1.3 60.2 + - - +
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Residues in contact with TYR 208 (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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121D VAL* 4.2 0.9 - - - -
122D CYS* 3.3 19.2 - - + -
123D LEU 3.4 27.6 - - - -
124D PRO* 3.6 13.2 - - + -
125D ASP* 4.7 5.8 + - - -
128D THR* 4.0 23.7 + - + -
129D LEU* 5.1 0.2 - - - -
200D VAL* 2.9 7.5 - - - -
201D MET* 2.8 38.0 + - + +
203D SER* 3.7 22.9 - - - -
204D ASN* 2.9 26.6 - + + -
206D ARG* 3.1 34.7 - - + -
207D TRP* 1.3 75.0 - - - +
209D GLN* 1.3 59.2 + - - +
210D MET* 3.3 21.1 + - - +
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Residues in contact with GLN 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* 2.6 32.4 + - - -
47D ILE* 4.1 1.9 - - - +
53D LEU* 3.7 18.8 + - + +
121D VAL* 3.7 18.3 - - + +
122D CYS 2.9 16.0 + - - +
123D LEU* 4.5 4.3 - - + -
124D PRO* 3.1 21.2 - - - +
196D GLY 5.2 1.0 + - - -
197D GLY 4.4 1.0 + - - -
198D PRO* 3.2 25.8 - - + +
199D PHE 3.5 5.2 - - - +
200D VAL* 4.1 4.7 - - + -
208D TYR* 1.3 71.1 - - - +
210D MET* 1.3 60.0 + - - +
211D GLY 3.2 21.2 + - - +
212D ILE* 4.0 12.7 - - - +
231D VAL* 3.5 14.0 - - + +
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Residues in contact with MET 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* 3.7 26.5 - - + -
128D THR* 4.2 8.5 - - - +
129D LEU* 3.6 35.9 - - + +
130D LEU* 3.7 32.8 - - + +
181D PHE* 3.6 9.0 - - - -
199D PHE* 2.7 19.3 + - + +
201D MET* 3.5 36.3 - - + +
208D TYR* 3.3 16.6 + - - +
209D GLN* 1.3 73.1 - - - +
211D GLY* 1.3 56.2 + - - +
230D HIS* 3.9 3.3 + - + -
231D VAL* 2.9 23.8 + - - +
232D PHE* 4.4 3.1 + - + -
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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* 3.9 9.0 - - - -
199D PHE* 2.9 37.5 + - - +
209D GLN* 3.2 13.6 + - - +
210D MET* 1.3 81.4 - - - +
212D ILE* 1.3 65.2 + - - -
228D TYR* 4.5 0.7 - - - -
229D THR 3.0 12.1 - - - -
231D VAL* 3.5 2.7 - - - -
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Residues in contact with ILE 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 LEU* 4.0 11.0 - - + -
54D THR 3.5 9.0 - - - +
55D ALA* 3.8 16.6 - - + +
102D ASP 4.6 0.7 - - - +
103D ILE* 3.4 42.8 - - + -
196D GLY* 3.5 33.4 - - - +
197D GLY 3.4 3.8 - - - +
209D GLN* 4.0 9.9 - - - +
211D GLY* 1.3 79.4 - - - +
213D VAL* 1.3 64.2 + - - +
214D SER* 2.8 11.1 + - - -
228D TYR* 3.2 6.4 - - - +
229D THR* 3.0 34.2 + - - -
231D VAL* 4.0 11.9 - - + -
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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* 3.9 3.1 - - - +
138D VAL* 3.7 29.2 - - + -
139D THR 5.2 0.2 - - - +
190D ALA* 4.0 19.3 - - + -
191D CYS 4.5 0.4 - - - +
194D ASP* 3.2 33.9 - - + +
195D SER* 3.3 8.7 - - - +
196D GLY* 2.8 26.3 + - - -
197D GLY* 2.9 18.5 + - - +
198D PRO 4.7 2.7 - - - +
211D GLY 4.3 0.2 - - - -
212D ILE* 1.3 68.4 - - - +
214D SER* 1.3 59.0 + - - +
215D TRP 4.5 0.9 - - - +
216D GLY* 4.2 16.2 - - - +
228D TYR* 3.8 19.2 - - + -
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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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221B ARG* 5.1 0.2 - - - +
55D ALA* 5.0 0.4 - - - -
57D HIS* 3.0 25.3 + - - -
99D LEU* 3.9 18.5 + - - +
102D ASP* 2.9 32.0 + - - +
180D MET* 6.1 2.3 - - - -
192D GLU* 4.9 1.0 - - - +
195D SER* 4.1 2.9 + - - -
212D ILE 2.8 4.9 + - - -
213D VAL* 1.3 73.7 - - - +
215D TRP* 1.3 63.7 + - - +
216D GLY 4.2 0.4 - - - -
227D PHE* 2.9 22.3 + - - +
228D TYR* 4.0 2.7 - - - -
229D THR* 3.8 17.9 - - - -
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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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221B ARG* 3.4 67.3 + - + -
222B ASP* 3.6 24.9 - - + -
98D ASN 5.9 2.0 - - - -
99D LEU* 4.8 10.3 - - + -
174D ILE* 3.1 28.7 - - + -
192D GLU* 4.5 5.2 - - - -
195D SER* 5.2 0.7 - - - -
213D VAL* 4.8 0.7 - - - -
214D SER* 1.3 80.2 - - - +
216D GLY* 1.3 70.4 + - - +
217D LYS* 3.3 27.2 - - + +
221D ASP* 3.5 14.0 + - - -
226D GLY* 3.4 4.7 - - - -
227D PHE* 2.8 57.3 + + + -
228D TYR* 6.2 0.2 - - - -
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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