Contacts of the strand formed by residues 124 - 129 (chain D) in PDB entry 3T0E
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 GLU 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D PRO* 4.9 4.9 - - + +
123D PRO* 1.3 72.1 - - - +
125D VAL* 1.3 61.3 + - - +
126D ALA* 3.9 0.7 + - - +
146D LEU 3.4 5.5 - - - +
148D THR* 2.7 41.9 + - - +
149D GLY* 5.1 3.6 - - - +
187D ARG* 5.7 3.4 - - - +
235D VAL* 5.1 0.7 - - - -
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LYS* 5.4 1.4 - - - +
123D PRO* 3.7 6.6 + - + -
124D GLU* 1.3 72.5 - - - +
126D ALA* 1.3 64.7 + - - +
145D CYS* 4.1 21.3 - - - -
146D LEU 3.8 2.5 - - - +
147D ALA* 3.5 26.7 - - + -
210D CYS* 4.5 2.9 - - - +
212D VAL* 3.6 20.0 - - + -
235D VAL* 4.0 26.6 - - + +
236D SER* 3.7 6.5 - - - +
237D ALA* 3.2 36.3 + - + +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ASP* 4.7 2.7 - - - +
125C LYS* 3.7 24.7 - - + -
127C SER* 4.5 13.7 - - - +
124D GLU 3.9 0.8 + - - +
125D VAL* 1.3 76.5 - - - +
127D VAL* 1.3 65.0 + - - +
128D PHE* 4.8 5.8 - - + -
145D CYS* 3.9 3.5 - - - -
146D LEU* 3.1 34.6 + - + +
237D ALA* 3.4 9.0 - - - -
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ASP* 3.4 18.0 - - - +
124C SER* 3.9 18.8 + - - +
125C LYS 5.1 0.6 - - - +
126D ALA* 1.3 76.2 - - - +
128D PHE* 1.3 91.3 + - - +
129D GLU* 4.5 1.1 - - - +
143D LEU* 4.5 19.5 - - + -
144D VAL 3.4 13.0 - - - +
145D CYS* 4.5 1.3 - - - +
159D TRP* 4.8 6.7 - - + -
208D PHE 5.8 0.2 - - - +
210D CYS* 4.3 12.3 - - + +
237D ALA* 3.3 11.9 - - + +
238D GLU* 3.3 39.3 - - - +
239D ALA* 5.8 2.0 - - + -
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 4.0 11.5 - - + +
122C ARG 3.8 3.4 - - - -
123C ASP* 3.6 25.4 - - + -
124C SER 4.8 0.4 - - - +
128C ASP* 3.5 35.0 - - + -
130C SER* 4.4 4.0 - - - -
131C VAL* 3.2 48.5 - - + -
126D ALA* 4.9 5.6 - - + -
127D VAL* 1.3 86.7 - - - +
129D GLU* 1.3 62.3 + - - +
143D LEU* 3.5 6.6 - - - +
144D VAL* 2.7 52.8 + - + +
146D LEU* 3.8 28.7 - - + -
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 3.5 5.1 - - - +
122C ARG* 3.2 42.2 + - + +
123C ASP 4.8 6.2 - - - +
124C SER* 3.5 22.8 + - - +
127D VAL* 4.5 1.3 - - - +
128D PHE* 1.3 73.5 - - - +
130D PRO* 1.3 85.3 - - + +
143D LEU* 5.0 2.5 - - - -
201D TRP* 3.6 28.0 - - + -
239D ALA* 4.6 5.0 - - + +
242D ARG* 2.9 36.6 + - - +
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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