Contacts of the strand formed by residues 190 - 197 (chain L) in PDB entry 1MHP
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 190 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148L LYS 4.5 0.9 - - - +
149L VAL* 3.3 10.9 - - - +
150L ASP* 2.8 55.8 + - - +
151L ASN* 3.9 16.2 - - - +
189L LYS* 1.3 84.2 - - + +
191L TYR* 1.3 62.5 + - - +
192L ALA* 5.9 1.8 - - + -
207L SER* 5.7 4.5 - - - -
208L PHE 3.4 3.8 - - - +
209L ASN* 3.1 26.0 - - - +
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Residues in contact with TYR 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L ILE* 3.9 2.9 - - - +
131L VAL* 4.5 7.9 - - + -
147L TRP* 5.1 1.3 - - + -
148L LYS 3.8 1.3 - - - -
149L VAL* 3.5 32.1 - - + -
178L LEU* 4.1 11.0 - - + -
180L LEU* 3.8 16.7 - - + +
184L ASP 3.7 0.9 + - - -
185L TYR* 2.8 73.4 + + - -
188L HIS* 3.3 25.9 - - + +
189L LYS 4.0 7.0 - - - -
190L VAL* 1.3 73.9 - - - +
192L ALA* 1.3 61.1 + - - +
207L SER* 3.2 21.2 - - - -
208L PHE* 3.0 38.6 + + + -
210L ARG* 4.1 8.1 - - + -
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Residues in contact with ALA 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L ILE* 4.1 1.3 - - - -
147L TRP* 3.2 14.3 - - - -
148L LYS* 2.9 45.1 + - + +
190L VAL* 5.6 2.5 - - + -
191L TYR* 1.3 77.0 - - - +
193L CYS* 1.3 61.6 + - - +
194L GLU 4.3 0.2 - - - -
205L THR* 4.1 11.9 - - + -
206L LYS 3.3 6.1 - - - +
207L SER* 3.3 19.5 - - - -
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Residues in contact with CYS 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L VAL* 5.5 0.7 - - - +
116L ILE* 3.9 18.8 - - - -
133L CYS* 2.0 53.8 - - + -
145L VAL* 3.9 11.4 - - + -
146L GLN 3.3 4.3 - - - +
147L TRP* 4.0 11.2 - - + -
192L ALA* 1.3 76.0 - - - +
194L GLU* 1.3 61.6 + - - +
195L VAL* 3.9 2.4 + - - +
204L VAL 3.7 1.0 - - - +
205L THR* 3.5 3.9 - - - -
206L LYS* 3.0 34.0 + - - +
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Residues in contact with GLU 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L LYS 3.6 1.0 - - - +
145L VAL* 3.5 5.7 - - - +
146L GLN* 3.0 56.9 + - + +
148L LYS* 3.2 30.4 + - - +
192L ALA 4.3 0.4 - - - -
193L CYS* 1.3 73.8 - - - +
195L VAL* 1.3 60.0 + - - +
196L THR* 4.6 3.3 + - - +
203L PRO* 3.4 36.6 - - + +
204L VAL 3.1 4.7 - - - +
205L THR* 3.5 17.5 + - + +
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Residues in contact with VAL 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L PRO* 4.2 10.8 - - + -
114L VAL* 3.6 29.2 - - + -
133L CYS* 4.4 8.1 - - - -
135L LEU* 3.6 43.3 - - + -
144L LYS 3.6 2.9 - - - +
145L VAL* 4.3 3.6 - - + -
193L CYS 4.6 2.2 - - - +
194L GLU* 1.3 75.1 - - - +
196L THR* 1.3 72.3 + - - +
197L HIS* 4.6 1.1 - - + -
200L LEU* 4.0 20.6 - - + +
203L PRO* 3.0 8.0 - - - +
204L VAL* 2.6 36.7 + - + +
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Residues in contact with THR 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142L GLU 4.5 0.2 - - - +
143L ALA* 3.8 4.5 - - - -
144L LYS* 3.1 56.7 + - - +
146L GLN* 4.6 4.3 + - - -
194L GLU* 4.6 4.2 + - - -
195L VAL* 1.3 77.2 - - - +
197L HIS* 1.3 64.3 + - - +
200L LEU* 5.4 0.2 - - - -
202L SER 5.6 0.2 - - - -
203L PRO* 3.6 30.9 - - + +
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Residues in contact with HIS 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L ALA 3.7 11.0 - - - -
112L PRO* 3.8 23.8 - - + +
138L PHE* 3.4 20.7 - + + -
139L TYR 3.2 27.6 - - - -
140L PRO* 2.8 33.0 + - + +
142L GLU 3.3 23.1 + - - -
143L ALA* 4.2 7.0 - - + -
195L VAL* 4.6 1.8 - - + -
196L THR* 1.3 77.0 - - - +
198L GLN* 1.3 58.4 + - - +
199L GLY* 2.9 26.1 + - - +
200L LEU* 2.7 44.1 + - + +
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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