Contacts of the strand formed by residues 22 - 27 (chain D) in PDB entry 2Q2U
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 CYS 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D VAL* 4.2 7.9 - - - -
19D GLN 3.5 17.5 - - - +
20D PHE* 4.3 0.9 - - - -
21D PRO* 1.3 76.0 - - - +
23D LEU* 1.3 61.3 + - - +
24D ALA* 5.1 1.3 - - - -
141D GLU* 3.7 3.3 - - - +
142D ILE* 2.7 59.3 + - - +
148D LEU* 5.4 2.0 - - - -
165D ILE* 3.4 28.3 - - + -
166D ARG 3.4 14.8 - - - +
167D LYS* 5.2 0.9 - - - -
168D PRO* 4.1 6.1 - - + -
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Residues in contact with LEU 23 (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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22D CYS* 1.3 76.2 - - - +
24D ALA* 1.3 60.5 + - - +
25D THR* 5.4 0.4 - - - +
109D TYR* 3.6 27.8 - - + -
110D ILE* 3.4 33.0 - - + -
139D PRO* 3.5 25.6 - - + +
140D VAL 3.2 23.3 - - - +
141D GLU* 3.8 20.2 - - + +
164D MET 3.8 0.3 - - - +
165D ILE* 3.7 1.0 - - - +
166D ARG* 2.8 36.3 + - - +
168D PRO* 4.1 18.1 - - + +
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Residues in contact with ALA 24 (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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22D CYS* 4.1 0.9 + - - -
23D LEU* 1.3 75.1 - - - +
25D THR* 1.3 69.2 + - - +
140D VAL* 2.7 31.7 + - - +
142D ILE* 3.9 20.2 - - + -
148D LEU* 5.4 2.5 - - + -
151D TYR* 3.8 15.7 + - + -
163D VAL* 3.7 17.7 - - + -
164D MET 3.2 11.9 - - - +
165D ILE* 4.6 7.9 - - + -
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Residues in contact with THR 25 (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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23D LEU 5.4 0.2 - - - -
24D ALA* 1.3 82.2 - - - +
26D PRO* 1.3 77.4 + - - +
98D PHE* 5.3 4.1 - - + +
109D TYR* 3.9 12.8 - - + +
137D LEU* 3.9 18.3 - - + +
138D ILE 4.2 2.0 - - - -
139D PRO* 3.3 29.4 - - + -
151D TYR* 3.1 9.0 - - - -
163D VAL* 3.2 5.4 - - - +
164D MET* 2.7 46.3 + - - +
166D ARG* 5.7 3.3 + - + +
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Residues in contact with PRO 26 (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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25D THR* 1.3 97.9 + - - +
27D LYS* 1.3 60.7 + - - +
28D ILE* 3.3 14.2 - - + +
137D LEU* 3.8 28.0 - - + +
138D ILE 6.0 0.7 - - - +
151D TYR* 3.0 12.1 - - - +
155D VAL* 3.7 12.1 - - + -
160D PHE* 3.6 42.8 - - + -
162D GLY 3.7 6.1 - - - +
164D MET* 4.5 1.8 - - - +
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Residues in contact with LYS 27 (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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25D THR 3.7 1.0 + - - -
26D PRO* 1.3 71.8 - - - +
28D ILE* 1.3 78.3 + - - +
29D ASP* 4.9 0.2 - - - +
30D GLY 5.4 0.6 + - - -
67D GLU* 3.4 18.4 + - - -
160D PHE* 4.0 3.5 - - - +
161D GLU* 3.1 65.9 + - + +
162D GLY* 3.0 24.4 + - - +
163D VAL 4.0 0.4 - - - +
164D MET* 3.4 40.8 - - + +
186D LYS* 5.7 3.1 - - + +
188D LYS* 5.1 4.9 - - + +
31L C 4.5 1.8 + - - -
32L C 3.3 23.8 + - - -
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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