Contacts of the strand formed by residues 158 - 162 (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 SER 158 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147L TRP* 3.8 29.2 - - - -
154L GLN* 6.2 1.3 - - - -
155L SER 5.8 1.0 + - - -
156L GLY 3.9 4.4 + - - +
157L ASN* 1.3 75.7 - - - +
159L GLN* 1.3 72.4 - - - +
160L GLU* 5.6 2.3 - - - +
176L SER* 4.5 4.5 + - - -
177L THR 3.1 14.6 - - - -
178L LEU* 4.3 4.0 - - - -
179L THR* 4.8 1.6 - - - +
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Residues in contact with GLN 159 (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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174H VAL* 3.8 23.7 - - + +
175H LEU 3.1 27.2 + - - +
176H GLN* 3.8 19.5 - - - +
177H SER 4.9 3.7 - - - +
157L ASN* 6.4 0.2 - - + -
158L SER* 1.3 86.4 + - - +
160L GLU* 1.3 66.1 + - - +
175L SER* 3.4 3.1 + - - +
177L THR* 3.0 36.0 + - - +
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Residues in contact with GLU 160 (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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174H VAL* 3.9 14.3 - - - +
143L ALA 4.9 4.3 - - - +
144L LYS* 5.2 0.5 - - - -
145L VAL* 3.7 31.0 + - - +
158L SER* 5.6 2.5 - - - +
159L GLN* 1.3 76.5 - - - +
161L SER* 1.3 63.0 + - - +
174L LEU* 3.5 30.9 - - + +
175L SER 3.0 7.0 - - - +
176L SER* 3.7 20.4 + - - +
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Residues in contact with SER 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H PHE* 3.5 6.3 - - - +
172H PRO* 2.9 46.3 + - - +
174H VAL* 4.0 12.1 - - - -
160L GLU* 1.3 77.9 - - - +
162L VAL* 1.3 60.9 + - - +
174L LEU* 3.4 4.0 - - - +
175L SER* 2.9 42.9 + - - -
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Residues in contact with VAL 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H PRO* 3.4 18.6 - - - +
138L PHE* 5.7 1.1 - - + -
141L ARG* 3.0 47.1 - - + +
161L SER* 1.3 78.2 + - - +
163L THR* 1.3 77.3 + - - +
172L TYR* 4.4 13.7 - - + -
173L SER 3.4 10.8 - - - +
174L LEU* 4.3 16.4 - - + +
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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