Contacts of the strand formed by residues 198 - 207 (chain D) in PDB entry 3IT8
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 MET 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D GLY 4.4 5.8 - - - +
191D ASN 4.1 5.4 - - - +
192D GLU* 3.5 16.6 - - + +
193D LEU 5.5 0.2 - - - -
196D GLY 5.3 1.2 - - - -
197D ASN* 1.3 85.3 + - + +
199D THR* 1.3 69.6 + - - +
200D LEU* 4.9 1.3 - - - -
270D ARG* 3.9 6.4 - - - -
271D THR* 2.9 51.5 + - + +
278D GLN* 3.7 20.4 - - - +
296D SER* 3.7 6.7 - - - -
297D GLU* 3.0 49.1 - - - +
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Residues in contact with THR 199 (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 THR 3.5 0.2 - - - +
190D GLY* 3.3 5.0 - - - -
191D ASN* 3.1 55.6 + - + +
192D GLU* 3.7 2.9 - - - +
193D LEU* 4.0 31.2 - - + +
198D MET* 1.3 77.9 + - - +
200D LEU* 1.3 61.6 + - - +
268D LEU* 3.8 26.7 - - + +
269D VAL 3.2 15.2 + - - -
270D ARG* 4.6 4.4 - - - +
271D THR* 4.0 0.2 - - - -
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Residues in contact with LEU 200 (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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188D VAL* 3.9 15.7 - - + -
189D THR 3.3 12.6 - - - +
190D GLY* 3.9 3.6 - - - -
198D MET* 4.9 2.2 - - - -
199D THR* 1.3 73.8 - - - +
201D GLU* 1.3 60.4 + - - +
202D CYS 4.2 0.7 - - - -
216D TRP* 3.8 17.4 - - + -
267D ASP 3.9 0.5 - - - +
268D LEU* 3.3 4.8 - - - +
269D VAL* 2.7 42.6 + - + +
271D THR* 3.5 16.3 + - - +
278D GLN* 4.0 5.4 - - + +
279D PRO* 3.4 48.0 - - + +
295D CYS 4.1 0.7 - - - +
296D SER* 2.9 35.2 - - - +
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Residues in contact with GLU 201 (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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187D LYS 3.6 1.9 - - - +
188D VAL* 3.2 5.1 - - - -
189D THR* 2.7 45.0 + - - +
191D ASN* 3.5 23.2 + - - +
200D LEU* 1.3 73.7 - - - +
202D CYS* 1.3 60.7 + - - +
203D THR* 3.4 21.6 + - + +
266D THR* 3.9 26.9 + - + +
267D ASP 3.4 2.9 - - - +
268D LEU* 3.4 23.2 - - + +
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Residues in contact with CYS 202 (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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186D VAL* 4.0 20.9 - - - -
187D LYS 3.8 3.1 - - - -
188D VAL* 4.1 4.7 - - - +
201D GLU* 1.3 72.6 - - - +
203D THR* 1.3 62.1 + - - +
204D VAL* 4.2 5.4 + - + +
214D THR* 4.2 2.0 - - - -
216D TRP* 3.3 17.8 - - + -
265D LEU* 4.1 0.9 - - - +
266D THR* 3.6 0.9 - - - -
267D ASP* 2.7 44.1 + - + +
281D CYS* 2.0 50.0 - - + -
283D VAL* 4.0 6.3 - - - -
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Residues in contact with THR 203 (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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185D THR 3.4 1.4 - - - +
186D VAL* 3.3 5.9 - - - +
187D LYS* 3.0 41.5 + - + +
189D THR* 5.2 4.9 - - - +
201D GLU* 3.4 32.3 - - + +
202D CYS* 1.3 76.8 - - - +
204D VAL* 1.3 60.0 + - - +
205D ASN* 3.6 20.8 + - - -
265D LEU 3.4 10.3 - - - -
266D THR* 4.2 7.9 - - - +
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Residues in contact with VAL 204 (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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184D PRO* 3.2 36.6 - - + -
185D THR 3.4 2.9 - - - -
186D VAL* 4.1 10.5 - - + -
202D CYS* 4.7 5.6 - - - +
203D THR* 1.3 75.7 - - - +
205D ASN* 1.3 60.9 + - - +
207D PHE* 3.5 18.6 - - + -
212D VAL* 4.8 3.4 - - + -
214D THR* 5.5 0.9 - - - +
264D SER* 3.5 4.3 - - - -
265D LEU* 2.9 57.4 + - + +
283D VAL* 4.0 32.5 - - + -
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Residues in contact with ASN 205 (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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184D PRO* 3.0 19.9 - - - +
185D THR* 2.7 31.5 + - - +
187D LYS* 4.2 22.6 - - - +
203D THR* 3.6 21.3 + - - -
204D VAL* 1.3 77.7 - - - +
206D SER* 1.3 76.8 + - - +
207D PHE 3.8 0.4 - - - -
264D SER* 3.8 10.5 + - - +
265D LEU 5.3 0.3 - - - +
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Residues in contact with SER 206 (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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182D THR* 3.3 16.9 - - - +
183D THR 3.6 6.6 - - - +
205D ASN* 1.3 80.1 + - - +
207D PHE* 1.3 57.2 + - - +
257D ASP* 3.2 15.3 - - - -
258D LYS* 4.6 9.1 + - - -
262D THR* 2.6 27.5 + - - -
263D TYR 2.8 9.7 + - - -
264D SER* 3.0 10.5 + - - -
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Residues in contact with PHE 207 (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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182D THR 3.1 11.2 - - - +
184D PRO* 3.5 17.3 - - + -
204D VAL* 3.5 32.1 - - + -
206D SER* 1.3 73.6 - - - +
208D TYR* 1.3 63.4 + - - +
209D PRO 3.5 13.2 - - - -
210D PRO* 3.6 17.7 - - + -
212D VAL* 3.4 28.0 - - + -
254D ILE* 4.3 6.5 - - + -
262D THR* 2.7 6.3 + - - -
263D TYR* 2.8 53.5 + - + -
264D SER 4.0 1.6 - - - -
265D LEU* 3.7 32.3 - - + -
285D HIS* 3.7 10.5 - - + -
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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