Contacts of the strand formed by residues 129 - 133 (chain H) in PDB entry 3KDM
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 129 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B SER 4.6 10.0 + - - -
123B ALA* 5.8 0.2 - - - -
124B SER* 4.4 12.8 + - - -
126H LYS* 4.9 4.0 + - - -
127H GLY 4.0 0.2 + - - -
128H PRO* 1.3 73.8 - - - +
130H VAL* 1.3 59.7 + - - +
131H PHE* 3.7 29.2 - - - -
150H LEU 3.4 2.6 - - - +
151H VAL* 3.7 0.7 - - - -
152H LYS* 3.0 38.3 + - - +
153H ASP* 5.7 2.0 + - - +
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Residues in contact with VAL 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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128H PRO* 4.1 10.1 + - + +
129H SER* 1.3 76.4 - - - +
131H PHE* 1.3 63.0 + - - +
149H CYS* 4.2 5.4 - - + -
150H LEU 3.3 7.9 - - - +
151H VAL* 4.4 5.2 - - + -
205H CYS* 4.0 7.4 - - - -
207H VAL* 3.9 45.1 - - + -
216H VAL* 3.9 22.9 - - + +
218H LYS* 3.2 50.8 - - + +
127L GLU* 3.4 8.8 - - - +
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Residues in contact with PHE 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 SER* 3.7 35.4 - - - -
130H VAL* 1.3 80.7 - - - +
132H PRO* 1.3 69.8 - - - +
149H CYS* 3.3 4.7 - - - -
150H LEU* 2.8 55.8 + - + +
152H LYS* 4.6 7.9 - - + -
218H LYS* 5.0 0.7 - - - -
125L SER* 3.4 24.0 - - - +
127L GLU* 3.9 18.8 - - + -
128L GLN* 3.5 51.6 - - + +
131L SER* 5.1 8.1 - - - -
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Residues in contact with PRO 132 (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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130H VAL 4.6 0.4 - - - +
131H PHE* 1.3 91.1 - - + +
133H LEU* 1.3 65.9 + - - +
134H ALA* 3.6 10.1 + - + +
148H GLY 3.7 5.6 - - - +
149H CYS* 4.5 4.5 - - - -
218H LYS* 4.8 7.6 - - + -
219H LYS 3.6 25.4 - - - +
220H ALA* 4.1 10.5 - - - -
221H GLU 5.1 0.7 - - - +
123L PRO 4.8 2.4 - - - +
125L SER* 3.7 29.5 + - - -
127L GLU* 3.8 17.3 - - + +
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Residues in contact with LEU 133 (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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132H PRO* 1.3 77.2 - - - +
134H ALA* 1.3 66.4 + - - +
147H LEU* 3.2 5.7 - - - +
148H GLY* 2.8 46.3 + - - +
149H CYS 3.9 16.4 - - - +
150H LEU* 4.1 13.9 - - + +
188H SER* 3.7 29.2 - - - +
190H VAL* 4.4 9.0 - - + -
220H ALA* 3.9 0.7 - - - +
122L PHE* 3.7 35.2 - - + +
123L PRO 4.8 6.7 - - - +
135L SER 5.7 2.0 - - - +
137L VAL* 3.9 26.9 - - + -
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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