Contacts of the strand formed by residues 127 - 131 (chain B) in PDB entry 5DK3
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B LYS* 5.0 8.0 + - - +
126B PRO* 1.3 74.3 - - - +
128B VAL* 1.3 58.3 + - - +
129B PHE* 3.6 32.1 - - - -
148B LEU 3.5 2.1 - - - +
149B VAL* 3.5 2.3 - - - -
150B LYS* 2.9 39.0 + - - +
151B ASP* 5.7 0.7 - - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLU* 3.4 20.2 + - - +
126B PRO* 4.1 6.3 + - + +
127B SER* 1.3 76.8 - - - +
129B PHE* 1.4 63.0 + - - +
147B CYS* 4.2 5.4 - - + -
148B LEU 3.4 5.2 - - - +
149B VAL* 4.5 7.9 - - + -
203B CYS* 3.9 17.5 - - - -
205B VAL* 3.9 35.0 - - + -
214B VAL* 4.0 27.5 - - + +
216B LYS* 3.5 36.8 - - + -
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A SER* 3.6 23.1 - - - +
127A GLU* 3.9 22.0 - - + -
128A GLN* 3.5 52.7 - - + +
131A SER* 5.2 5.4 - - - -
127B SER* 3.6 32.1 - - - -
128B VAL* 1.4 79.5 - - - +
130B PRO* 1.3 66.2 - - - +
131B LEU* 6.1 0.4 - - + -
147B CYS* 3.4 2.9 - - - -
148B LEU* 2.7 60.7 + - + +
150B LYS* 4.5 12.1 - - + -
216B LYS* 4.6 2.2 - - - -
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO 5.0 3.1 - - - +
125A SER* 4.0 27.0 + - - -
127A GLU* 3.8 18.2 - - + +
129B PHE* 1.3 87.4 - - + +
131B LEU* 1.4 63.8 - - - +
132B ALA* 3.9 5.3 + - + +
146B GLY 3.7 5.4 - - - +
147B CYS* 4.6 1.8 - - - -
216B LYS* 4.1 10.1 - - + -
217B ARG 4.1 8.3 - - - +
218B VAL* 4.0 32.3 - - + +
224G PRO* 5.8 7.9 - - + -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 3.6 31.2 - - + -
123A PRO 5.1 5.4 - - - +
135A SER 5.8 1.3 - - - +
137A VAL* 3.9 38.4 - - + -
129B PHE* 6.1 0.2 - - + -
130B PRO* 1.4 75.6 - - - +
132B ALA* 1.4 59.3 + - - +
145B LEU* 3.3 11.1 - - - +
146B GLY* 2.7 46.9 + - - +
147B CYS 3.6 25.6 - - - +
148B LEU* 4.0 18.4 - - + +
186B SER* 4.8 6.1 - - - +
187B SER 4.4 2.9 - - - +
188B VAL* 4.4 8.3 - - + -
218B VAL* 3.5 2.8 - - - +
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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