Contacts of the strand formed by residues 121 - 126 (chain A) in PDB entry 1X1R
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 MET 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.0 19.7 - - + +
90A ILE* 3.9 16.6 - - + -
107A HIS* 3.5 33.7 - - + -
110A ILE* 3.5 41.1 - - + -
111A LEU* 4.3 12.6 - - + -
119A PHE 3.1 18.4 + - - +
120A PRO* 1.3 75.1 - - - +
122A ILE* 1.3 69.1 + - - +
150A ILE* 3.6 26.9 - - + +
151A PRO* 3.4 17.0 - - - +
171A LEU* 3.9 3.6 - - - +
174A VAL* 4.4 5.0 - - - +
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Residues in contact with ILE 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 PHE 3.0 5.9 + - - -
89A LEU* 3.7 13.6 - - + -
90A ILE* 3.0 27.8 + - - +
121A MET* 1.3 80.9 - - - +
123A LEU* 1.3 64.7 + - - +
124A VAL* 3.7 5.3 + - + +
150A ILE* 4.3 3.8 - - - -
151A PRO* 3.8 28.0 - - + +
153A ILE* 3.7 30.1 - - + -
167A THR* 4.0 4.7 - - + +
170A ASP* 3.4 22.9 - - + +
171A LEU* 3.3 38.1 - - + +
174A VAL* 4.2 6.5 - - + -
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Residues in contact with LEU 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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90A ILE* 3.6 16.8 - - + +
92A TYR* 3.8 27.4 - - + -
103A VAL* 3.7 28.3 - - + -
122A ILE* 1.3 72.3 - - - +
124A VAL* 1.3 59.9 + - - +
125A ALA 4.0 0.2 + - - -
141A GLY* 3.5 25.1 - - - +
144A MET* 3.7 18.8 - - + -
145A ALA* 3.8 15.0 - - + +
148A TYR* 5.4 0.4 - - + -
150A ILE* 3.9 16.4 - - + +
151A PRO 3.0 15.0 + - - +
152A TYR* 3.5 8.2 - - + -
153A ILE 3.0 26.5 + - - +
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Residues in contact with VAL 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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29A LEU* 4.2 16.6 - - + -
89A LEU* 4.1 16.2 - - + -
90A ILE 2.9 14.3 + - - +
91A VAL* 3.4 9.7 - - + +
92A TYR* 2.9 31.9 + - - +
122A ILE* 3.9 12.1 - - + +
123A LEU* 1.3 76.7 - - - +
125A ALA* 1.3 58.8 + - - +
153A ILE* 3.4 6.7 - - + +
155A THR* 3.4 37.5 - - + +
167A THR* 3.7 26.5 - - + -
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Residues in contact with ALA 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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92A TYR* 3.4 34.1 - - + +
94A VAL* 3.8 11.4 - - + -
123A LEU 4.0 1.0 + - - -
124A VAL* 1.3 69.0 - - - +
126A ASN* 1.3 63.2 + - - +
128A VAL* 3.5 5.4 - - - +
152A TYR* 3.5 25.1 - - + +
153A ILE 2.9 10.8 + - - +
154A GLU* 3.3 5.6 - - + -
155A THR* 2.9 23.5 + - - -
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Residues in contact with ASN 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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24A VAL 2.9 27.6 + - - +
25A GLY* 3.6 7.5 + - - -
29A LEU* 3.5 18.1 - - - +
91A VAL* 4.0 11.2 - - + -
92A TYR 2.8 14.0 + - - +
93A SER* 3.6 0.3 - - - -
94A VAL* 3.0 28.4 + - - +
125A ALA* 1.3 74.8 - - - +
127A LYS* 1.3 75.4 + - - +
128A VAL 3.4 1.6 - - - -
155A THR* 2.8 30.9 + - - +
156A SER* 3.6 0.3 - - - -
1179A GDP 3.3 32.1 + - - +
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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