Contacts of the strand formed by residues 174 - 186 (chain K) in PDB entry 5D4C
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 VAL 174 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44K LEU* 3.2 27.6 - - + +
45K LEU* 4.4 9.5 - - + +
48K ILE* 4.0 26.2 - - + -
172K SER* 3.2 13.9 + - - +
173K PRO* 1.3 77.7 - - + +
175K ARG* 1.3 63.3 + - - +
176K ARG 4.0 3.8 - - - +
177K VAL* 3.5 31.6 - - + -
199K ILE* 4.4 6.1 - - + -
200K TRP 3.7 10.5 - - - +
201K THR* 4.0 11.9 - - + -
210K ALA* 4.4 8.1 - - + -
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Residues in contact with ARG 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K LEU* 4.8 5.3 - - - +
84K GLU* 4.5 9.9 + - - +
86K VAL* 3.7 18.2 - - - +
173K PRO 3.4 2.0 + - - +
174K VAL* 1.3 76.4 - - - +
176K ARG* 1.3 62.3 + - + +
200K TRP* 2.8 20.0 + - + +
201K THR 3.8 18.8 - - - -
202K ASP* 3.5 29.7 + - + +
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Residues in contact with ARG 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K LEU* 4.6 4.0 - - - -
174K VAL* 3.6 1.0 - - - -
175K ARG* 1.3 80.3 - - + +
177K VAL* 1.3 73.8 + - - +
198K ARG* 5.5 0.2 - - - +
200K TRP* 2.9 81.6 + - + +
863M ASP* 3.0 33.6 + - - +
864M GLY 4.2 14.6 - - - +
865M THR* 3.7 24.6 + - - +
866M PRO* 5.4 2.2 - - - -
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Residues in contact with VAL 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K ARG* 3.2 55.6 + - + -
44K LEU* 3.7 29.4 - - + -
45K LEU* 4.1 14.1 - - + +
174K VAL* 3.5 22.0 - - + -
176K ARG* 1.3 84.2 - - - +
178K ALA* 1.3 70.4 + - - +
197K LEU* 4.6 5.4 - - + -
198K ARG 3.5 8.1 - - - +
199K ILE* 4.5 7.0 - - + -
864M GLY* 3.5 13.5 + - - +
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Residues in contact with ALA 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K ARG* 4.7 4.5 - - - +
177K VAL* 1.3 77.2 - - - +
179K PHE* 1.3 65.9 + - - +
197K LEU* 3.7 4.7 - - - +
198K ARG* 2.9 41.3 + - + +
200K TRP* 4.4 6.7 - - + -
860M HIS* 5.9 2.0 - - + -
862M PRO 3.8 8.7 - - - +
863M ASP* 3.5 33.4 - - - +
864M GLY* 3.6 3.8 - - - +
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Residues in contact with PHE 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K GLY 3.8 13.5 - - - -
34K VAL* 4.0 9.2 - - - -
37K GLY* 3.7 13.0 - - - -
38K ASN* 3.5 43.1 - - + -
41K ARG* 4.3 16.4 - - + -
178K ALA* 1.3 79.9 - - - +
180K GLN* 1.3 65.7 + - - +
181K VAL* 4.1 4.0 - - + -
195K LEU* 3.7 21.1 - - + -
196K THR 3.1 11.7 - - - +
197K LEU* 3.7 14.6 - - + -
198K ARG* 5.6 0.4 - - - -
860M HIS* 5.3 4.8 - + - -
862M PRO 4.6 6.3 + - - +
939M ARG* 3.4 50.0 + - - -
975M TYR* 5.0 2.6 - - - -
980M GLY* 4.4 6.1 - - - -
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Residues in contact with GLN 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K PHE* 1.3 77.2 - - - +
181K VAL* 1.3 63.0 + - - +
182K GLU* 3.7 23.6 - - + +
194K LYS 3.1 5.0 - - - +
195K LEU* 3.6 1.6 - - - -
196K THR* 2.9 44.5 + - - +
198K ARG* 6.0 2.2 - - + -
862M PRO* 4.6 7.8 - - - +
929M ARG* 3.6 30.3 + - - +
934M PHE* 4.2 18.6 - - + +
935M GLY 2.6 29.5 + - - -
936M VAL 4.1 0.4 - - - -
937M ASP* 3.5 17.7 - - - +
975M TYR* 5.7 1.0 + - - -
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Residues in contact with VAL 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K GLY* 3.6 31.9 - - - +
34K VAL* 3.9 7.6 - - + +
179K PHE* 4.1 6.3 - - + -
180K GLN* 1.3 73.9 - - - +
182K GLU* 1.3 62.7 + - - +
193K ASP* 3.4 37.2 - - + +
194K LYS 3.5 2.9 - - - +
195K LEU* 4.3 1.3 - - + -
937M ASP* 2.7 19.9 + - - +
938M LYS* 3.0 41.3 + - + +
939M ARG* 3.9 15.9 - - - +
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Residues in contact with GLU 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K GLN* 3.7 23.6 - - + -
181K VAL* 1.3 75.2 - - - +
183K ASP* 1.3 66.5 + - - +
184K THR 3.5 0.2 + - - -
192K LEU 3.7 1.9 - - - +
193K ASP* 3.9 1.0 - - - -
194K LYS* 2.9 69.4 + - + +
196K THR* 3.9 9.0 + - - -
933M GLY 4.4 1.4 - - - +
934M PHE* 3.6 15.8 - - - +
935M GLY* 3.0 29.6 + - - +
936M VAL 4.3 15.0 - - - +
938M LYS* 4.3 2.9 - - - -
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Residues in contact with ASP 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K GLU* 1.3 76.9 - - - +
184K THR* 1.3 71.8 + - - +
191K ASP* 3.4 25.0 + - - -
192K LEU 3.2 9.0 - - - +
194K LYS* 5.1 1.6 - - - +
936M VAL 5.4 1.2 + - - -
938M LYS* 3.5 23.7 - - + +
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Residues in contact with THR 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K GLU* 3.8 13.6 + - - +
27K PRO* 4.1 14.9 - - + +
183K ASP* 1.3 82.0 + - - +
185K ARG* 1.3 75.3 + - - +
191K ASP 4.0 1.9 + - - -
192K LEU* 2.9 54.5 + - + +
193K ASP 3.6 19.5 - - - +
194K LYS* 3.7 13.9 - - + +
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Residues in contact with ARG 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K PRO* 5.6 0.7 - - - -
184K THR* 1.3 86.3 + - - +
186K LEU* 1.3 60.4 + - - +
187K GLY 2.7 29.1 + - - +
188K GLN* 4.1 15.8 - - - +
189K ARG 3.4 14.6 - - - +
190K THR* 3.3 31.7 - - + +
192K LEU* 4.5 3.8 - - - -
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Residues in contact with LEU 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 4.3 20.2 - - + -
27K PRO* 3.9 27.4 - - + -
185K ARG* 1.3 75.8 - - - +
187K GLY* 1.3 70.7 + - - +
188K GLN 3.4 0.5 + - - -
189K ARG* 3.2 31.7 + - - +
192K LEU* 3.9 15.8 - - + +
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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