Contacts of the strand formed by residues 24 - 30 (chain A) in PDB entry 2UVQ
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 PHE 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 4.2 3.6 - - - +
23A PRO* 1.3 68.2 - - - +
25A LEU* 1.3 60.9 + - - +
26A ILE* 3.6 32.8 + - + -
133A ASP 2.7 15.2 + - - +
134A VAL* 3.3 8.6 - - + +
135A VAL 2.9 25.0 + - - -
153A HIS* 3.2 40.2 - + + -
154A LEU* 4.1 14.4 - - + -
226A HIS* 4.1 17.7 - + - -
230A ILE* 3.4 37.9 - - + -
235A ILE* 6.6 0.2 - - + -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO* 3.5 7.4 + - + +
24A PHE* 1.3 70.8 - - - +
26A ILE* 1.3 61.2 + - - +
27A GLY 3.9 0.2 - - - -
101A LEU* 3.3 34.3 - - + -
104A ILE* 4.6 8.1 - - + -
105A VAL* 3.6 25.1 - - + -
135A VAL* 3.3 39.3 - - + +
137A PHE* 5.7 1.1 - - + -
151A MET* 3.6 27.8 - - + +
152A PHE* 3.6 14.6 - - + -
153A HIS* 2.8 38.8 + - + +
154A LEU 3.4 5.0 + - - -
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.6 28.9 + - + -
25A LEU* 1.3 70.6 - - - +
27A GLY* 1.3 66.0 + - - +
28A VAL* 4.1 3.4 - - + +
134A VAL* 4.1 7.6 - - + -
135A VAL 2.9 8.0 + - - +
136A LEU* 3.4 20.6 - - + -
137A PHE* 2.9 26.3 + - - -
152A PHE* 4.1 1.8 - - - -
154A LEU* 3.4 23.3 - - + +
156A LEU* 3.8 28.7 - - + -
223A ILE* 4.3 6.3 - - + -
226A HIS* 5.7 1.1 - - + -
227A ILE* 3.7 36.6 - - + -
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 1.3 74.0 - - - +
28A VAL* 1.3 56.6 + - - +
137A PHE 3.5 7.6 - - - -
143A PHE* 3.5 10.8 - - - -
152A PHE* 3.4 30.8 - - - -
154A LEU 3.0 10.0 + - - +
155A ARG* 3.5 0.7 - - - -
156A LEU* 2.7 34.7 + - - +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.1 19.3 - - + +
27A GLY* 1.3 77.0 - - - +
29A SER* 1.3 62.4 + - - +
36A LYS* 4.0 9.2 - - + +
39A VAL* 5.5 5.8 - - + -
40A CYS* 4.0 23.3 - - - -
43A ILE* 6.6 0.2 - - + -
136A LEU* 4.7 5.2 - - + -
137A PHE 2.9 16.6 + - - +
138A GLU* 3.2 8.7 - - + +
139A GLY 3.1 23.7 + - - +
142A VAL* 4.0 2.3 - - - +
143A PHE* 4.2 0.2 - - - -
156A LEU* 3.3 20.9 - - + +
158A VAL* 4.0 25.6 - - + -
210A ILE* 5.8 0.7 - - + -
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 1.3 74.8 - - - +
30A GLY* 1.3 62.3 + - - +
36A LYS* 3.4 17.2 - - - +
139A GLY 2.6 21.5 + - - -
140A ILE 3.4 14.6 + - - -
142A VAL* 3.8 8.8 + - - -
143A PHE* 3.5 32.0 + - - -
156A LEU 2.8 10.0 + - - -
157A PHE* 4.2 7.7 - - - -
158A VAL* 3.2 20.0 + - - +
202A THR* 4.7 3.7 + - - -
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 1.3 81.6 + - - +
31A GLY* 1.3 64.3 + - - -
34A SER* 3.4 2.9 - - - -
36A LYS* 2.8 18.1 - - - -
140A ILE* 3.6 12.9 + - - +
157A PHE* 3.7 18.1 - - - -
158A VAL 3.6 17.0 - - - -
199A CYS* 4.1 7.0 - - - -
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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