Contacts of the strand formed by residues 114 - 121 (chain A) in PDB entry 3SRG
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 PRO 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLU* 5.4 0.2 - - - +
66A SER* 3.8 12.2 + - - -
67A SER* 3.4 22.9 + - - +
68A GLY 4.8 0.9 - - - +
69A LEU* 3.6 20.3 + - - +
83A GLY* 3.6 20.0 - - - -
84A LYS 3.8 13.9 - - - +
85A ILE* 3.9 0.9 - - + -
112A PHE* 3.7 16.6 - - + -
113A ASN* 1.3 92.9 - - - +
115A HIS* 1.3 60.6 + - - +
131A VAL* 3.6 21.8 - - + -
132A VAL 3.3 7.0 - - - +
133A ASN* 4.5 1.3 - - - +
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Residues in contact with HIS 115 (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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53A GLU* 3.4 22.9 - - - -
54A ASP* 3.8 1.9 - - - +
66A SER* 2.9 23.2 + - - -
69A LEU* 3.8 13.0 - - + +
71A TYR* 3.7 15.5 - + - -
114A PRO* 1.3 74.1 - - - +
116A GLY* 1.3 75.0 + - - +
117A ILE* 3.7 0.3 - - - +
131A VAL* 4.4 0.2 - - - +
132A VAL* 2.9 15.6 + - + -
134A HIS* 2.9 36.3 + + + +
167A VAL 3.7 4.0 + - - -
168A ASN* 3.4 34.2 + - - -
183A ASP* 4.2 0.2 - - - -
1358A OCH 2.8 35.4 + + - -
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Residues in contact with GLY 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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53A GLU* 4.1 2.5 - - - -
54A ASP* 3.4 11.0 - - - -
115A HIS* 1.3 84.2 - - - +
117A ILE* 1.4 61.4 + - - +
132A VAL* 2.9 32.4 + - - +
168A ASN 3.1 16.8 + - - -
169A ASP* 3.4 19.3 - - - -
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Residues in contact with ILE 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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54A ASP* 2.8 20.9 + - - +
55A LEU* 3.7 12.3 - - - +
56A GLU* 3.8 15.8 - - + +
64A PHE* 3.5 40.8 - - + +
65A ILE 4.7 0.2 - - - -
66A SER* 3.8 18.4 - - - +
85A ILE* 4.5 2.7 - - + -
115A HIS 3.7 9.4 - - - +
116A GLY* 1.4 80.7 - - - +
118A SER* 1.3 63.8 + - - +
129A LEU* 4.3 9.2 - - + -
130A LEU 3.1 13.2 - - - +
131A VAL* 4.1 16.6 - - + -
169A ASP* 3.2 2.1 + - - +
170A ILE* 3.7 3.6 - - - -
1356A CA 2.4 28.9 - - - -
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Residues in contact with SER 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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56A GLU* 3.4 15.1 + - - -
117A ILE* 1.3 78.2 - - - +
119A THR* 1.3 67.7 + - - +
129A LEU* 3.6 4.6 - - - +
130A LEU* 2.9 30.8 + - - +
170A ILE* 3.4 24.5 - - - -
171A VAL* 3.5 8.0 - - - +
172A ALA* 2.8 32.6 + - - +
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Residues in contact with THR 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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56A GLU* 2.6 35.2 + - + +
58A LEU* 4.0 23.5 - - + +
64A PHE* 3.9 20.6 - - + -
118A SER* 1.3 82.8 + - - +
120A PHE* 1.3 64.8 + - - +
121A ILE* 5.2 3.0 - - - +
127A VAL* 4.8 2.5 - - + -
128A TYR 3.2 9.0 - - - +
129A LEU* 3.8 19.5 - - + -
130A LEU* 5.1 0.2 - - - -
172A ALA* 3.6 14.8 - - - +
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Residues in contact with PHE 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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119A THR* 1.3 76.6 - - - +
121A ILE* 1.3 79.9 + - - +
122A ASP* 3.7 24.9 - - - -
126A THR 3.5 2.3 - - - +
127A VAL* 3.7 0.4 - - - -
128A TYR* 2.8 43.8 + + + +
130A LEU* 4.9 0.8 - - + +
172A ALA* 3.9 9.2 - - + -
173A VAL* 3.6 22.2 - - - -
174A GLY* 3.6 43.5 - - - +
175A PRO* 3.8 13.9 - - + -
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Residues in contact with ILE 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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58A LEU* 4.4 15.9 - - + -
59A PRO* 3.8 33.4 - - + -
119A THR* 5.2 2.7 - - - +
120A PHE* 1.3 91.3 - - - +
122A ASP* 1.3 75.6 + - - +
125A ASN* 3.8 24.0 - - + +
126A THR 3.3 9.4 - - - +
127A VAL* 4.4 15.9 - - + -
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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