Contacts of the strand formed by residues 127 - 131 (chain H) in PDB entry 4M7L
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 127 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126H PRO* 1.3 73.5 + - - +
128H VAL* 1.3 64.1 + - - +
129H PHE* 3.3 34.7 - - - -
148H LEU 2.8 15.5 - - - +
149H VAL* 3.4 2.8 - - - -
150H LYS* 2.6 31.6 + - - +
151H ASP* 5.3 4.9 - - - -
133L SER* 5.2 2.1 + - - -
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Residues in contact with VAL 128 (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 PRO* 4.4 9.8 + - + +
127H SER* 1.3 80.9 + - - +
129H PHE* 1.3 62.8 + - - +
147H CYS* 3.9 9.0 - - + -
148H LEU 3.3 3.6 - - - +
149H VAL* 4.0 14.1 - - + -
203H CYS* 3.7 30.1 - - - +
205H VAL* 4.0 15.9 - - + -
214H VAL* 3.8 30.6 - - + +
216H LYS* 3.0 35.1 + - + +
129L GLU* 4.9 0.2 - - - +
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Residues in contact with PHE 129 (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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127H SER* 3.3 37.5 - - - -
128H VAL* 1.3 78.6 - - - +
130H PRO* 1.3 74.2 - - + +
131H LEU* 4.5 0.9 - - + +
147H CYS* 3.3 22.0 - - - +
148H LEU* 3.3 21.8 + - + +
150H LYS* 4.7 13.9 - - + -
216H LYS* 4.4 2.9 - - - -
127L SER* 4.2 11.9 - - - +
129L GLU* 3.8 14.4 - - + -
130L GLN* 3.5 63.0 - - + +
133L SER* 4.2 11.0 - - - -
135L THR* 5.2 4.0 - - - -
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Residues in contact with PRO 130 (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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129H PHE* 1.3 90.3 - - + +
131H LEU* 1.3 65.1 + - - +
132H ALA 3.8 3.5 + - - +
146H GLY 3.8 4.3 - - - +
147H CYS* 4.8 0.2 - - - -
216H LYS* 3.8 12.5 - - + -
217H LYS 4.2 6.3 - - - +
218H VAL* 4.1 26.0 - - + -
219H GLU 4.5 7.6 - - - +
125L PRO 5.4 1.0 - - - +
126L PRO 5.2 0.3 - - - -
127L SER* 3.5 29.5 + - - +
129L GLU* 3.3 33.2 - - - +
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Residues in contact with LEU 131 (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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129H PHE* 5.1 0.7 - - + +
130H PRO* 1.3 75.0 - - - +
132H ALA* 1.3 66.3 + - - +
133H PRO* 3.3 9.0 - - - +
145H LEU* 3.4 15.2 - - - +
146H GLY* 2.8 25.6 + - - +
147H CYS* 3.2 37.0 - - - +
148H LEU* 4.1 9.2 - - + +
186H SER* 4.4 9.6 - - - -
188H VAL* 3.8 15.5 - - + -
218H VAL* 3.6 3.7 - - - +
124L PHE* 3.8 37.9 - - + +
125L PRO 5.3 3.8 - - - +
126L PRO* 6.3 1.8 - - + -
139L VAL* 4.7 16.6 - - + -
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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