Contacts of the strand formed by residues 120 - 128 (chain A) in PDB entry 2EA3
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 GLY 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PRO* 4.0 11.0 - - - +
116A THR* 4.3 4.7 - - - -
117A TYR* 2.9 37.4 + - - +
118A PRO 3.3 0.4 - - - -
119A GLU* 1.3 80.0 - - - +
121A THR* 1.3 64.6 + - - -
122A VAL 3.8 0.9 + - - -
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Residues in contact with THR 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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53A PRO* 3.5 2.5 - - - +
54A GLY* 2.8 30.5 + - - -
114A SER* 4.4 8.3 - - - -
115A VAL 3.2 14.8 - - - +
116A THR* 3.3 21.6 + - - +
120A GLY* 1.3 72.5 - - - -
122A VAL* 1.3 63.8 + - - +
123A ARG* 4.1 38.5 + - + +
192A SO4 5.4 1.8 - - - -
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Residues in contact with VAL 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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52A PHE* 3.7 13.5 - - + -
53A PRO* 4.0 2.2 - - + -
54A GLY 3.5 14.8 - - - +
55A ASN 3.6 28.7 - - - +
56A ASP* 4.1 4.3 - - + +
114A SER* 3.2 4.0 - - - -
115A VAL* 2.9 31.5 + - + +
117A TYR* 3.6 33.7 - - + -
121A THR* 1.3 77.9 - - - +
123A ARG* 1.3 65.2 + - - +
125A LEU* 3.7 32.7 - - + +
152A SER* 4.8 0.2 - - - +
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Residues in contact with ARG 123 (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 GLY* 2.9 28.3 + - - +
55A ASN* 4.8 5.4 + - - -
112A ASN* 5.2 1.6 - - - +
113A SER 3.7 4.3 - - - -
114A SER* 3.2 19.9 + - - +
121A THR* 4.1 32.0 + - + +
122A VAL* 1.3 83.5 - - - +
124A GLY* 1.3 65.4 + - - +
125A LEU* 3.3 6.5 + - - +
167A GLN* 5.0 2.1 - - - +
192A SO4 3.0 39.7 + - - -
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Residues in contact with GLY 124 (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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112A ASN* 2.9 33.8 + - - -
113A SER 3.2 5.3 + - - -
114A SER* 4.8 0.2 + - - -
123A ARG* 1.3 78.0 - - - +
125A LEU* 1.3 60.4 + - - +
167A GLN* 5.2 0.3 + - - -
168A PRO* 3.2 27.6 - - - +
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Residues in contact with LEU 125 (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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111A LEU 3.6 1.0 - - - -
112A ASN 3.1 8.7 + - - -
113A SER* 2.8 39.1 + - - +
115A VAL* 3.7 32.8 - - + -
122A VAL* 3.7 34.8 - - + +
123A ARG 3.9 5.8 - - - +
124A GLY* 1.3 79.1 - - - +
126A ILE* 1.3 62.5 + - - +
152A SER* 4.4 11.0 - - - +
165A PHE* 3.8 26.2 - - + -
166A PHE 3.4 22.2 - - - +
167A GLN* 3.7 17.3 - - + +
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Residues in contact with ILE 126 (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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108A ILE* 3.9 33.2 - - + -
110A ALA 3.6 4.0 - - - +
111A LEU* 4.1 15.7 - - + +
112A ASN 5.9 0.2 - - - +
125A LEU* 1.3 70.7 - - - +
127A ARG* 1.3 61.9 + - - +
128A THR* 3.9 15.3 - - + -
141A LEU* 4.6 4.3 - - + -
148A GLN* 3.7 39.7 - - + +
164A THR 3.7 0.9 - - - +
165A PHE* 3.1 7.0 - - - -
166A PHE* 2.7 51.5 + - + +
168A PRO* 4.0 22.2 - - + -
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Residues in contact with ARG 127 (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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108A ILE* 3.6 2.1 - - - +
109A THR* 2.8 43.8 + - - +
110A ALA* 2.8 23.8 + - + +
113A SER* 3.5 20.9 - - - +
125A LEU 3.6 2.4 + - - -
126A ILE* 1.3 72.6 - - - +
128A THR* 1.3 62.7 + - - +
163A THR* 3.7 28.5 + - + +
165A PHE* 3.4 41.9 - - + -
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Residues in contact with THR 128 (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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94A VAL* 4.3 11.9 - - + -
107A THR 3.2 13.7 - - - +
108A ILE* 4.2 4.9 - - - -
109A THR* 4.2 4.7 - - - -
126A ILE* 3.9 13.7 - - + -
127A ARG* 1.3 81.3 - - - +
129A THR* 1.3 61.7 + - - +
130A VAL* 3.0 20.9 + - - +
141A LEU* 4.5 1.1 - - + -
163A THR* 3.4 12.7 - - - +
164A THR 2.9 36.1 + - - -
166A PHE* 3.3 33.7 - - + -
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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