Contacts of the strand formed by residues 123 - 128 (chain D) in PDB entry 2Q41
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 LYS 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D LYS* 1.3 81.2 - - + +
124D VAL* 1.3 60.6 + - - +
145D GLU* 6.3 0.2 - - + -
146D GLN* 3.7 32.5 - - + +
148D ASP* 2.9 27.1 + - - -
194D SER* 3.0 33.7 - - - +
195D TYR* 3.6 26.0 + - + -
196D ASP* 2.9 37.4 + - - +
197D ALA 3.3 5.5 + - - -
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Residues in contact with VAL 124 (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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115D LEU* 3.9 16.6 - - + -
121D PRO* 5.0 1.6 - - + -
122D LYS 3.9 0.2 + - - -
123D LYS* 1.3 79.6 - - - +
125D LEU* 1.3 66.5 + - - +
126D VAL* 4.1 21.3 - - + -
138D VAL* 4.3 15.3 - - + -
144D ILE* 3.7 37.2 - - + -
146D GLN 3.4 7.5 + - - +
147D ILE* 3.7 5.3 - - + -
148D ASP 3.1 26.2 + - - +
195D TYR* 3.6 6.9 - - - -
197D ALA* 3.6 10.5 - - + +
199D ILE* 4.6 13.2 - - + -
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Residues in contact with LEU 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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124D VAL* 1.3 75.6 - - - +
126D VAL* 1.3 77.8 + - - +
127D ILE* 4.2 19.3 - - + -
148D ASP* 3.3 16.2 - - + +
150D CYS* 4.6 4.0 - - + +
186D PHE* 3.7 33.2 - - + -
187D LEU* 3.3 35.2 - - + -
195D TYR* 3.5 21.5 - - + -
197D ALA 3.1 10.2 + - - +
198D VAL* 3.4 13.1 - - + +
199D ILE* 2.8 27.5 + - - +
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Residues in contact with VAL 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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124D VAL* 4.1 17.3 - - + -
125D LEU* 1.3 80.6 - - - +
127D ILE* 1.3 69.5 + - - +
128D GLY 4.5 3.4 - - - +
134D VAL* 3.9 35.7 - - + -
135D LEU* 4.9 4.5 - - + -
138D VAL* 4.3 6.1 - - + -
147D ILE* 4.7 8.1 - - + -
148D ASP 2.8 12.1 + - - +
149D MSE 4.2 19.3 - - + -
150D CYS 2.6 32.1 + - - -
199D ILE* 3.4 13.7 - - + +
201D ASP* 4.7 8.3 - - + +
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Residues in contact with ILE 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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125D LEU* 4.2 17.7 - - + -
126D VAL* 1.3 80.8 - - - +
128D GLY* 1.3 60.2 + - - +
150D CYS* 3.7 17.9 - - + +
183D GLY* 4.3 23.1 - - - +
186D PHE* 6.3 0.2 - - + -
187D LEU* 4.0 13.7 - - + -
198D VAL* 4.7 6.1 - - + -
199D ILE 3.0 11.4 + - - +
200D VAL* 4.5 5.8 - - + -
201D ASP 3.0 27.6 + - - -
202D SER* 3.5 2.4 + - - -
212D LEU* 4.6 21.5 - - + -
217D PHE* 3.8 32.8 - - + -
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Residues in contact with GLY 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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126D VAL* 4.1 3.8 - - - +
127D ILE* 1.3 77.1 - - - +
129D GLY* 1.3 61.5 + - - +
149D MSE 3.0 24.8 - - - +
150D CYS 3.4 9.8 + - - -
151D GLU* 3.8 12.7 - - - +
201D ASP* 3.6 18.6 - - - -
202D SER* 4.7 2.7 - - - -
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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