Contacts of the strand formed by residues 120 - 124 (chain J) in PDB entry 3Q3G
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 THR 120 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118J ALA 4.6 3.1 + - - -
119J PRO* 1.4 70.1 - - - +
121J VAL* 1.3 60.8 + - - +
122J SER* 4.6 6.8 + - - +
141J PHE* 3.2 5.0 - - - +
143J ASN* 2.9 43.9 + - + +
144J ASN* 5.2 4.6 + - - +
213J LYS* 6.3 0.2 - - - +
148K THR* 5.3 2.9 - - - +
611K EDO 4.5 24.2 - - - +
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Residues in contact with VAL 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J PRO* 3.7 14.6 + - + +
120J THR* 1.3 74.7 - - - +
122J SER* 1.3 65.6 + - - +
140J CYS* 3.7 13.9 - - - -
141J PHE 3.2 2.5 - - - -
142J LEU* 3.7 24.2 - - + -
200J CYS* 4.0 6.7 - - - +
202J ALA* 3.8 22.2 - - + -
211J ILE* 3.8 26.3 - - + +
213J LYS* 2.8 56.1 + - + +
611K EDO 4.5 1.0 + - - -
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Residues in contact with SER 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J THR* 4.6 6.1 + - - +
121J VAL* 1.3 75.8 - - - +
123J ILE* 1.3 60.6 + - - +
124J PHE* 3.8 27.2 - - - -
139J VAL 3.8 0.5 - - - +
140J CYS* 3.2 5.1 - - - -
141J PHE* 2.9 36.8 + - - +
143J ASN* 5.9 0.2 + - - -
213J LYS* 4.7 2.2 - - - +
148K THR* 3.9 17.5 + - - +
611K EDO 3.3 23.4 + - - -
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Residues in contact with ILE 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J SER* 1.3 73.9 - - - +
124J PHE* 1.3 74.2 + - - +
125J PRO* 4.4 3.0 - - + +
138J VAL* 4.2 3.6 - - + -
139J VAL 3.4 9.2 - - - +
140J CYS* 4.5 0.4 - - - +
154J TRP* 3.8 24.2 - - + -
198J TYR 3.4 25.6 - - - +
200J CYS* 4.0 11.9 - - - +
213J LYS* 3.7 23.1 - - + +
214J SER 3.8 29.8 - - - +
215J PHE* 3.7 23.3 - - + -
137K PRO* 4.5 7.4 - - - +
138K GLY 4.6 2.3 + - - +
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Residues in contact with PHE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J SER* 3.8 24.9 - - - -
123J ILE* 1.3 79.4 - - - +
125J PRO* 1.3 71.6 - - + +
138J VAL* 3.5 5.5 - - - +
139J VAL* 2.8 43.4 + - + +
141J PHE* 3.4 36.8 - + - -
215J PHE* 4.3 3.8 - - - -
135K LEU* 3.8 41.8 - - + +
136K ALA 3.5 21.1 - - - +
137K PRO* 3.7 10.1 - - + -
148K THR* 3.3 33.0 - - + -
149K LEU* 4.3 2.0 - - - -
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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