Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 3CEI
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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116A LEU* 4.0 4.9 - - - -
118A GLY 3.8 2.4 + - - -
119A SER* 1.3 76.0 - - - +
121A TRP* 1.3 69.8 + - - -
138A THR 3.1 13.2 - - - -
140A ASN 3.6 7.2 - - - -
157A VAL* 2.9 33.0 + - - +
158A TRP* 3.4 13.5 - - - +
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Residues in contact with TRP 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLN* 3.1 20.3 + - - -
72A ASN* 3.3 50.1 - - + +
73A HIS* 3.5 26.9 - + - -
76A TYR* 3.9 10.1 - - + -
116A LEU* 3.1 9.5 - - - +
120A GLY* 1.3 75.4 - - - -
122A ASN* 1.3 61.4 + - - +
123A TRP* 3.4 24.6 - + + +
137A GLN* 3.4 1.2 - - - -
138A THR* 2.8 39.1 + - - +
140A ASN 2.8 29.0 + - - -
142A GLN 4.1 1.3 - - - -
154A VAL* 3.8 16.8 - - + -
155A VAL 3.6 4.9 - - - -
156A ASP* 3.4 49.4 - - + -
157A VAL* 4.3 0.2 - - - -
158A TRP* 3.5 3.6 - - - +
500A FE 4.4 0.2 - - - -
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Residues in contact with ASN 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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109A PHE* 3.0 61.3 + - - -
112A SER* 2.9 31.9 + - - +
113A ALA* 3.5 16.8 - - + +
116A LEU* 4.8 2.0 - - + -
121A TRP* 1.3 71.9 - - - +
123A TRP* 1.3 62.0 + - - +
135A ILE* 4.2 3.2 - - - +
136A ILE 3.7 2.9 - - - +
137A GLN* 3.8 9.0 - - - +
154A VAL* 3.3 1.6 - - - -
155A VAL* 3.0 44.8 + - + +
157A VAL* 4.8 1.7 - - + +
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Residues in contact with TRP 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 4.2 6.5 - + - -
72A ASN* 3.1 35.9 - - + -
75A PHE* 4.2 8.5 - + - -
109A PHE* 3.9 4.9 - - - -
121A TRP* 3.4 15.4 - - + +
122A ASN* 1.3 74.4 - - - +
124A ALA* 1.3 64.4 + - - +
125A ALA* 4.8 0.7 - - + -
135A ILE* 3.3 12.1 - - - +
136A ILE* 2.7 47.6 + - + +
138A THR* 3.0 25.0 + - + -
142A GLN 3.9 2.2 - - - -
143A THR* 3.2 23.3 - - - -
144A PRO* 3.2 29.7 - - + +
151A PRO* 3.6 35.2 - - + -
153A LEU 3.2 7.9 - - - -
154A VAL* 3.4 33.0 - - + -
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Residues in contact with ALA 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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105A PHE* 3.9 28.5 - - + -
109A PHE* 4.4 2.9 - - + -
123A TRP* 1.3 73.3 - - - +
125A ALA* 1.3 53.7 + - - +
133A ILE* 4.5 7.2 - - + -
134A GLU 3.2 8.5 - - - -
135A ILE* 4.5 0.9 - - - +
151A PRO* 3.7 0.9 - - - +
152A LEU* 2.7 40.0 + - + +
153A LEU* 2.9 26.4 + - + +
186A VAL* 6.2 0.2 - - + -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TRP* 4.0 0.4 - - + -
124A ALA* 1.3 76.1 - - - +
126A TYR* 1.3 62.6 + - - +
127A ASN 3.6 1.0 + - - -
133A ILE* 3.5 3.1 - - - +
134A GLU* 2.8 42.6 + - - +
136A ILE* 3.9 23.3 - - + -
144A PRO* 4.0 18.6 - - + -
149A LYS* 4.1 6.3 - - + -
150A VAL 3.2 17.5 - - - +
151A PRO* 4.2 3.1 - - + -
152A LEU* 4.3 2.5 - - - -
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Residues in contact with TYR 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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125A ALA* 1.3 70.5 - - - +
127A ASN* 1.3 69.9 + - - +
128A LEU* 3.6 29.5 + - + +
131A GLN* 3.2 52.0 + - + +
132A LYS 3.8 6.3 - - - -
133A ILE* 4.2 7.0 - - + +
149A LYS* 3.6 6.5 - - - -
150A VAL* 2.8 34.4 + - + +
152A LEU* 3.9 12.1 - - + +
190A TYR* 3.8 29.6 - + - -
193A ALA* 4.0 26.9 - - + -
194A LYS* 3.8 24.3 - - + +
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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