Contacts of the strand formed by residues 17 - 22 (chain C) in PDB entry 2R4H
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 17 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A SER* 3.7 1.1 - - - -
90A VAL* 2.8 62.5 + - + +
8C LEU* 3.8 14.8 - - + -
15C PHE* 3.7 18.6 - + + -
16C GLY* 1.3 78.7 - - - +
18C SER* 1.3 68.8 + - - +
19C LEU* 4.4 20.0 - - + -
31C VAL* 4.3 7.6 - - + -
33C ARG 3.2 13.2 - - - +
34C LEU* 4.1 6.7 - - + -
35C ALA 4.7 0.2 - - - +
40C ALA* 3.9 20.9 - - + -
46C MET* 4.1 11.0 - - + -
52C ILE* 4.4 5.6 - - + -
72C ILE* 4.4 9.2 - - + -
79C VAL* 4.5 5.2 - - + -
81C LEU* 3.8 26.0 - - + -
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Residues in contact with SER 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR 3.1 13.2 - - - -
89A SER* 2.9 22.3 + - - +
17C PHE* 1.3 78.2 - - - +
19C LEU* 1.3 62.7 + - - +
31C VAL* 3.7 5.2 - - - -
32C LEU* 3.0 28.1 + - - -
33C ARG* 3.0 49.2 + - - +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.0 5.3 - - - -
88A THR 2.8 37.5 + - - +
90A VAL* 5.2 2.2 - - + -
17C PHE* 4.4 9.6 + - + -
18C SER* 1.3 75.4 - - - +
20C ARG* 1.3 61.3 + - - +
29C LEU* 4.2 17.3 - - + -
30C TYR 3.3 11.2 - - - +
32C LEU* 4.7 0.9 - - - -
52C ILE* 3.6 26.5 - - + -
55C ILE* 4.7 2.7 - - + -
65C HIS* 3.2 36.9 - - + +
68C ALA* 4.5 7.9 - - + -
69C ILE* 3.4 24.5 - - + -
72C ILE* 4.1 22.2 - - + -
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.2 31.1 - - - +
48A ILE 2.8 26.7 + - - -
49A GLY* 4.2 2.4 - - - -
50A ASP* 3.6 18.2 + - - -
85A ARG 3.4 13.7 + - - +
86A GLY 3.5 13.0 - - - +
87A GLU* 3.3 22.6 + - + +
91A HIS 5.5 1.2 + - - -
19C LEU* 1.3 74.2 - - - +
21C GLY* 1.3 64.7 + - - +
27C MET* 3.5 25.0 - - + +
29C LEU* 3.3 6.6 - - - +
30C TYR* 2.8 71.7 + - + +
32C LEU* 4.1 19.5 - - + +
93C HIS* 4.5 2.8 - - - +
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY 3.5 4.8 + - - -
20C ARG* 1.3 78.7 - - - +
22C GLY* 1.3 59.4 + - - -
25C TYR* 3.6 12.2 - - - -
27C MET* 3.4 27.4 - - - -
28C ASP 4.1 1.3 - - - -
29C LEU* 3.2 7.5 - - - +
65C HIS* 2.6 34.5 + - - +
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY* 1.3 73.2 - - - -
23C ARG* 1.3 66.1 + - - -
24C GLU* 3.4 3.8 - - - -
25C TYR 3.1 11.5 + - - -
26C ASN 3.2 6.1 + - - -
27C MET 2.8 24.0 + - - +
29C LEU* 3.7 16.6 - - - +
63C MET 3.5 10.3 - - - -
65C HIS 4.0 5.2 - - - -
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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