Contacts of the strand formed by residues 114 - 122 (chain A) in PDB entry 3C9S
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 GLU 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LYS 3.0 9.2 + - - +
81A TRP* 3.3 8.9 - - + -
82A ALA* 2.8 26.0 + - - -
108A CYS* 4.3 5.6 - - - -
113A CYS* 1.3 81.8 - - - +
115A VAL* 1.3 74.2 + - - +
116A VAL* 3.4 21.9 + - + +
21B SER* 4.7 8.0 + - - -
22B LYS 5.5 1.2 + - - -
23B VAL* 4.3 13.5 - - - +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.0 10.8 - - + -
82A ALA* 3.2 13.0 - - + +
84A ILE* 4.3 9.9 - - + -
101A TYR* 4.6 9.9 - - + -
104A VAL* 3.5 29.8 - - + -
108A CYS* 3.7 13.4 - - - -
114A GLU* 1.3 83.6 - - - +
116A VAL* 1.3 60.7 + - - +
117A GLY 3.6 22.2 - - - +
900A ACP 4.6 0.9 - - + -
19B LEU* 3.7 36.4 - - + +
21B SER* 4.5 7.1 + - - -
24B ILE* 4.6 0.3 - - - +
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Residues in contact with VAL 116 (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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81A TRP* 4.2 11.4 - - + -
82A ALA 2.9 10.8 + - - +
83A LEU* 3.5 19.3 - - + -
114A GLU* 3.7 31.2 - - - +
115A VAL* 1.3 74.3 - - - +
117A GLY* 1.3 56.4 + - - +
900A ACP 4.5 0.5 + - - -
23B VAL* 3.5 21.5 - - + +
24B ILE* 3.4 17.7 + - - +
29B ALA* 3.3 27.8 - - + +
31B VAL* 4.1 19.7 - - + -
40B LEU* 4.1 17.7 - - + -
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Residues in contact with GLY 117 (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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83A LEU* 3.2 18.7 - - - +
84A ILE 3.1 15.9 + - - -
115A VAL* 3.5 8.2 - - - +
116A VAL* 1.3 81.8 - - - +
118A GLY* 1.3 57.7 + - - -
900A ACP 3.2 35.6 - - - -
24B ILE* 4.1 2.6 - - - +
29B ALA* 5.0 0.9 - - - -
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Residues in contact with GLY 118 (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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83A LEU* 3.9 3.6 - - - +
84A ILE 3.1 16.6 - - - -
117A GLY* 1.3 74.8 - - - -
119A ASN* 1.3 65.2 + - - +
900A ACP 3.1 35.3 + - - +
42B THR* 3.4 21.6 - - - +
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Residues in contact with ASN 119 (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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84A ILE 3.0 6.1 + - - -
85A SER* 3.7 14.5 + - - +
86A LEU 2.8 22.4 + - - -
118A GLY* 1.3 74.1 - - - -
120A ILE* 1.3 75.3 + - - +
121A SER* 3.3 22.6 + - - -
900A ACP 3.0 30.8 + - - -
42B THR* 3.2 15.9 - - + +
43B ASP* 4.0 3.2 - - - +
44B VAL* 3.7 17.8 - - + +
902B MG 2.5 28.2 - - - -
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Residues in contact with ILE 120 (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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86A LEU* 3.4 3.8 - - + -
88A LEU* 4.4 12.8 - - + -
119A ASN* 1.3 86.6 + - - +
121A SER* 1.3 64.8 + - - +
122A LYS* 6.3 2.5 - - - +
900A ACP 3.6 24.9 - - + +
8B GLU* 3.1 52.9 - - + +
11B LEU* 4.2 22.7 - - + -
12B ILE* 3.4 26.5 - - + -
15B ILE* 4.6 4.3 - - + -
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Residues in contact with SER 121 (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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86A LEU 2.8 6.6 + - - -
87A ASN* 3.3 20.5 - - - -
88A LEU* 2.7 34.7 + - - +
119A ASN* 3.3 19.9 + - - -
120A ILE* 1.3 71.8 + - - +
122A LYS* 1.3 62.5 + - - +
44B VAL* 3.6 14.4 - - - +
46B ASN* 3.8 12.3 - - - -
50B HIS* 4.9 9.5 - - - -
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Residues in contact with LYS 122 (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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88A LEU* 3.3 13.8 + - + +
90A GLU* 4.8 18.9 - - + +
120A ILE* 6.3 2.7 - - - +
121A SER* 1.3 79.8 - - - +
123A SER* 1.3 65.1 + - - +
3B LEU* 4.4 30.5 + - - +
4B LYS* 5.3 1.4 - - - +
7B GLY* 5.5 1.2 - - - -
8B GLU* 5.2 18.4 - - - +
11B LEU* 5.4 6.3 - - - +
46B ASN* 4.4 6.4 - - - +
49B VAL* 5.0 12.5 - - + +
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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