Contacts of the strand formed by residues 173 - 182 (chain D) in PDB entry 4GJ0
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 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D ASN* 3.0 20.8 + - - -
170D PHE 3.1 16.0 + - - +
171D GLN* 6.1 0.4 - - + -
172D ARG* 1.3 86.5 - - + +
174D CYS* 1.3 64.6 + - - +
175D TYR* 3.4 28.7 - - + +
200D SER* 3.0 16.0 + - - -
202D HIS* 5.4 3.2 - - - -
206D GLU* 2.8 21.0 + - - +
283D ASP* 2.8 39.3 + - - -
284D ARG 3.5 11.4 - - - +
285D LEU* 5.1 7.9 - - + -
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Residues in contact with CYS 174 (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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162D THR 3.5 9.2 - - - -
163D CYS* 2.0 57.9 - - + -
164D PRO* 4.1 3.1 - - + -
167D TRP* 3.6 8.5 - - + -
168D ILE 3.4 1.6 - - - -
173D LYS* 1.3 73.1 - - - +
175D TYR* 1.3 63.4 + - - +
283D ASP* 3.1 8.1 - - - +
284D ARG* 2.8 43.8 + - + +
285D LEU 4.0 4.5 - - - -
286D ALA* 3.6 17.9 - - - -
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Residues in contact with TYR 175 (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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166D LYS 4.3 0.7 - - - +
167D TRP* 3.2 11.6 - - - -
168D ILE* 2.8 42.5 + - - +
170D PHE* 3.7 22.3 + - + -
173D LYS* 3.4 37.7 - - + +
174D CYS* 1.3 75.1 - - - +
176D TYR* 1.3 58.6 + - - +
177D PHE* 3.9 21.4 - - + -
199D VAL* 3.9 12.8 - - + -
206D GLU* 2.6 37.4 + - + +
209D PHE* 3.3 25.1 - + + -
210D LEU* 3.6 25.1 - - + -
281D VAL* 4.6 2.0 - - + -
282D CYS 3.4 6.3 - - - +
283D ASP* 3.9 10.3 - - + -
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Residues in contact with TYR 176 (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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166D LYS* 3.8 34.5 - - + +
167D TRP* 3.4 36.3 - + + -
175D TYR* 1.3 73.9 - - - +
177D PHE* 1.3 65.2 + - - +
178D GLY* 3.4 26.7 + - - -
179D LYS 5.6 0.2 + - - -
194D MET* 3.3 38.0 - - + -
280D TRP* 3.9 11.9 - + - -
281D VAL* 3.4 7.7 - - - +
282D CYS* 3.0 34.6 + - + -
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Residues in contact with PHE 177 (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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166D LYS 5.3 1.0 + - - -
168D ILE* 4.1 23.8 - - + -
175D TYR* 3.9 18.2 - - + -
176D TYR* 1.3 79.8 - - - +
178D GLY* 1.3 65.8 + - - +
179D LYS* 4.0 9.0 + - - +
209D PHE* 4.1 18.8 - + - -
210D LEU* 4.1 18.4 - - + -
213D HIS* 3.3 50.7 - + + +
214D ALA* 4.1 7.4 - - - -
215D SER 5.3 1.6 - - - +
262D MET* 5.8 0.2 - - + -
280D TRP 3.9 2.9 - - - -
281D VAL* 3.8 27.4 - - + -
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Residues in contact with GLY 178 (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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176D TYR* 3.4 24.5 - - - -
177D PHE* 1.3 76.6 - - - +
179D LYS* 1.3 63.0 + - - +
279D ALA* 3.4 8.3 - - - +
280D TRP* 2.8 48.6 + - - -
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Residues in contact with LYS 179 (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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176D TYR* 5.6 0.2 + - - -
177D PHE 4.2 7.6 - - - +
178D GLY* 1.3 79.3 - - - +
180D GLY* 1.3 61.1 + - - +
182D LYS* 5.0 0.7 - - - -
215D SER* 6.2 2.2 - - - -
278D GLY 3.4 9.4 - - - +
279D ALA* 5.4 2.5 - - + -
280D TRP* 3.7 12.4 - - - -
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Residues in contact with GLY 180 (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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179D LYS* 1.3 74.8 - - - +
181D THR* 1.3 66.2 + - - -
182D LYS* 3.1 12.2 + - - +
277D LEU 3.4 6.0 - - - +
278D GLY* 3.1 10.8 + - - +
280D TRP* 3.0 20.4 + - - -
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Residues in contact with THR 181 (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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193A ASP* 4.1 17.0 + - - +
180D GLY* 1.3 68.4 - - - -
182D LYS* 1.3 65.2 + - - +
186D HIS* 4.3 2.4 + - - -
276D LYS* 4.3 29.8 + - + -
277D LEU 3.2 9.4 - - - +
278D GLY* 4.5 10.5 - - - -
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Residues in contact with LYS 182 (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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193A ASP* 3.5 4.9 - - - -
179D LYS 5.0 0.4 + - - -
180D GLY* 3.3 13.0 + - - +
181D THR* 1.3 80.4 + - - +
183D GLN* 1.3 67.1 + - - +
186D HIS* 3.6 19.5 + - + +
187D ALA* 3.8 24.9 - - + +
190D ALA* 3.9 5.4 - - + -
220D TRP* 2.9 20.4 + - - -
276D LYS* 3.9 2.9 - - - -
277D LEU 2.9 20.0 + - - +
280D TRP* 3.3 44.2 - - + +
301D GOL 2.6 44.5 + - - -
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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