Contacts of the strand formed by residues 199 - 205 (chain H) 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 TYR 199 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143H LEU* 3.7 34.8 - - + -
159H TRP* 4.4 4.7 - - + -
160H ASN* 3.6 2.2 - - - -
164H LEU* 3.5 28.2 - - + +
189H VAL* 3.2 42.1 - - + +
190H PRO* 4.5 1.4 - - - +
193H SER* 2.7 43.5 + - - -
194H LEU* 4.4 7.9 - - + -
197H GLN* 3.3 35.9 + - + +
198H THR* 1.3 74.8 + - - +
200H ILE* 1.3 62.9 + - - +
215H LYS* 3.8 2.9 + - - +
216H VAL* 2.9 39.7 + - - +
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Residues in contact with ILE 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H TRP* 3.2 10.9 - - - -
160H ASN* 2.8 46.7 + - - +
198H THR* 3.6 30.7 - - + +
199H TYR* 1.3 81.7 - - - +
201H CYS* 1.3 66.6 + - - +
202H ASN* 4.2 7.6 - - - +
213H ASP* 3.8 27.4 - - + -
214H LYS 3.4 12.6 - - - +
215H LYS* 4.3 20.4 - - + +
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Residues in contact with CYS 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H VAL* 4.7 0.7 - - - -
145H CYS* 2.0 51.1 - - + -
157H VAL* 4.8 4.5 - - + -
158H SER 3.6 4.7 - - - +
159H TRP* 3.5 23.8 - - + -
200H ILE* 1.3 72.6 - - - +
202H ASN* 1.3 61.5 + - - +
203H VAL* 4.1 13.2 - - - -
212H VAL 3.7 0.9 - - - +
213H ASP* 3.2 4.7 - - - -
214H LYS* 3.0 44.1 + - - -
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Residues in contact with ASN 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H THR* 3.7 1.9 + - - +
157H VAL* 3.2 5.9 - - - +
158H SER* 2.8 49.4 + - - +
160H ASN 3.4 7.0 + - - -
161H SER* 2.6 44.8 + - - +
200H ILE* 4.2 7.4 - - - +
201H CYS* 1.3 72.4 - - - +
203H VAL* 1.3 62.5 + - - +
204H ASN* 5.6 0.2 - - - -
211H LYS* 4.5 9.9 - - - +
213H ASP* 2.6 35.1 + - - +
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Residues in contact with VAL 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H PRO* 4.4 6.5 - - + -
126H VAL* 4.2 19.5 - - + -
145H CYS* 5.2 0.2 - - + -
147H VAL* 3.8 32.1 - - + -
155H VAL* 3.3 26.5 - - + -
156H THR 3.4 4.0 - - - +
157H VAL* 4.0 7.9 - - + -
201H CYS* 4.1 20.2 - - - -
202H ASN* 1.3 78.4 - - - +
204H ASN* 1.3 64.5 + - - +
205H HIS 5.0 0.2 - - - +
210H THR* 6.5 0.2 - - - -
211H LYS* 3.1 8.8 - - - +
212H VAL* 2.9 41.0 + - + +
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Residues in contact with ASN 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H PRO 4.4 0.3 - - - +
155H VAL* 3.8 4.2 - - - -
156H THR* 3.0 50.0 + - + +
203H VAL* 1.3 77.0 - - - +
205H HIS* 1.3 59.7 + - - +
206H LYS* 3.3 35.5 + - - +
210H THR 3.5 8.5 + - - +
211H LYS* 3.7 30.8 - - + +
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Residues in contact with HIS 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H LYS 3.7 3.1 + - - -
123H GLY* 3.8 12.3 - - - -
124H PRO* 3.5 25.1 - - + +
150H TYR* 3.9 12.3 - + - -
151H PHE 3.2 20.4 + - - -
152H PRO 2.9 28.9 - - - -
154H PRO 3.9 9.1 + - - -
155H VAL* 4.4 5.2 - - + +
203H VAL* 4.3 1.2 - - - +
204H ASN* 1.3 70.1 - - - +
206H LYS* 1.3 67.3 + - - +
207H PRO* 3.3 25.9 - - + +
208H SER* 2.6 45.8 + - - +
210H THR* 3.1 26.0 + - - +
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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