Contacts of the strand formed by residues 18 - 26 (chain A) in PDB entry 5UHC
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 ARG 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 2.7 52.1 + - + +
17A ASN* 1.3 82.6 - - + +
19A SER* 1.3 59.4 + - - +
20A GLN* 5.0 6.1 - - - +
175A THR* 6.0 0.2 - - - +
195A ASP* 2.7 35.1 + - - +
196A VAL 3.1 16.2 - - - +
197A GLU* 3.8 15.2 - - + +
204A PRO* 4.0 1.6 - - - -
996C ARG* 3.6 37.8 - - - +
997C ASP* 2.5 41.3 + - - -
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Residues in contact with SER 19 (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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12A ASP* 4.0 3.6 - - - -
13A VAL 3.7 6.7 - - - -
14A LEU* 3.5 30.9 - - - +
15A THR 4.4 0.4 - - - +
18A ARG* 1.3 75.3 - - - +
20A GLN* 1.3 63.4 + - - +
21A PHE* 3.1 31.4 - - - -
195A ASP* 4.8 0.9 - - - -
196A VAL 3.0 28.3 + - - +
204A PRO* 3.1 17.5 - - - +
205A ARG 4.4 0.2 + - - -
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Residues in contact with GLN 20 (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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12A ASP* 3.4 5.0 - - - +
13A VAL* 2.9 50.8 + - + +
18A ARG* 5.0 5.1 - - - +
19A SER* 1.3 71.3 - - - +
21A PHE* 1.3 61.6 + - - +
22A VAL* 4.1 2.7 + - + +
177A LYS* 4.8 13.0 + - - +
193A ILE* 3.3 26.2 - - + +
194A LEU 3.2 11.9 - - - +
195A ASP* 4.0 23.4 + - - +
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Residues in contact with PHE 21 (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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10A SER* 4.9 9.2 - - - +
11A GLU 3.6 13.2 - - - +
12A ASP* 3.4 18.6 - - + -
19A SER* 3.1 33.0 - - - -
20A GLN* 1.3 72.0 - - - +
22A VAL* 1.3 64.6 + - - +
23A ILE* 4.1 7.8 + - + +
192A LEU* 3.7 1.0 - - - +
193A ILE* 3.5 1.2 - - - -
194A LEU* 2.7 52.3 + - + +
196A VAL* 4.3 13.7 - - + -
204A PRO 3.8 9.9 - - - -
205A ARG* 3.6 31.4 - - + -
208A LEU* 3.5 34.3 - - + -
225B LEU* 4.5 12.3 - - + -
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Residues in contact with VAL 22 (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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9A LEU 4.0 0.3 - - - +
10A SER* 3.5 0.7 - - - -
11A GLU* 2.8 56.6 + - + +
13A VAL* 4.4 22.2 - - + -
20A GLN* 4.9 2.9 - - + +
21A PHE* 1.3 75.8 - - - +
23A ILE* 1.3 70.8 + - - +
24A GLU* 4.3 10.5 - - + +
191A LYS* 3.8 31.9 - - + -
192A LEU 3.3 9.0 - - - +
193A ILE* 4.6 16.2 - - + -
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Residues in contact with ILE 23 (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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8A THR* 4.8 6.3 - - - +
9A LEU 3.5 17.5 - - - +
10A SER* 4.3 14.8 - - - +
21A PHE* 5.0 9.2 - - + +
22A VAL* 1.3 82.1 - - - +
24A GLU* 1.3 63.5 + - - +
26A LEU* 3.5 33.6 - - + +
34A LEU* 5.1 4.7 - - + -
38A LEU* 5.2 12.3 - - + -
192A LEU* 2.8 50.5 + - + +
194A LEU* 6.3 2.9 - - + -
208A LEU* 6.1 4.0 - - + -
218B LEU* 5.1 9.4 - - + +
221B LEU* 5.4 7.2 - - + -
222B ALA* 6.2 2.0 - - + +
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Residues in contact with GLU 24 (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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8A THR* 4.3 2.2 - - - -
9A LEU* 2.9 33.9 + - + +
11A GLU* 3.9 21.0 - - + +
22A VAL* 4.8 6.4 - - + +
23A ILE* 1.3 78.7 - - - +
25A PRO* 1.3 76.6 - - + +
26A LEU 4.1 0.4 - - - +
189A PHE* 3.7 15.7 - - + -
190A ASP 4.4 0.2 - - - +
191A LYS* 3.5 39.6 - - + +
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Residues in contact with PRO 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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6A ARG* 3.8 46.9 - - + +
7A PRO 4.2 7.0 - - - +
8A THR* 3.1 29.8 - - + +
9A LEU* 5.7 1.6 - - + -
24A GLU* 1.3 87.4 - - + +
26A LEU* 1.3 61.6 + - - +
189A PHE* 3.8 26.0 - - + -
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Residues in contact with LEU 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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8A THR* 3.9 11.7 - - + -
23A ILE* 3.5 34.3 - - + +
25A PRO* 1.3 76.5 - - - +
27A GLU* 1.3 72.0 + - - +
28A PRO* 4.3 0.2 - - - +
30A PHE* 4.9 8.3 - - + -
31A GLY* 4.5 6.5 - - - +
34A LEU* 3.6 27.1 - - + -
189A PHE* 3.7 9.2 - - - +
190A ASP* 3.1 31.1 + - + +
192A LEU* 3.8 15.5 - - + -
218B LEU* 3.7 32.8 - - + -
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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