Contacts of the strand formed by residues 120 - 123 (chain A) in PDB entry 6AL5
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 GLU 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLN 4.7 7.6 - - - +
114A ASN* 4.9 4.0 - - - +
115A VAL 5.3 0.9 + - - +
118A SER* 3.0 27.7 + - - +
119A GLY* 1.3 86.1 + - - +
121A LEU* 1.3 71.6 + - - +
122A PHE* 3.7 23.9 - - + -
154A PRO* 4.8 0.2 - - - +
155A LYS* 3.4 15.9 - - + -
157A TYR* 4.9 9.2 - - + -
218A HIS* 3.1 36.0 + - - -
220A LYS* 5.0 0.5 - - - -
52H TRP* 5.1 4.3 + - - -
55H ASP* 3.7 21.1 - - - +
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Residues in contact with LEU 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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114A ASN* 3.8 10.1 - - + +
120A GLU* 1.3 81.8 - - - +
122A PHE* 1.3 64.0 + - - +
123A ARG* 3.6 25.8 - - - +
129A LEU* 3.8 21.1 - - + -
132A LEU* 4.6 13.9 - - + -
136A LEU* 4.9 11.0 - - + -
154A PRO* 4.3 25.6 - - + -
155A LYS 2.6 15.3 + - - +
156A LEU* 3.8 15.3 - - + -
157A TYR* 2.6 34.9 + - - +
189A THR* 6.4 0.7 - - + -
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Residues in contact with PHE 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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89A GLN 5.9 0.2 - - - -
92A GLY* 3.8 9.2 - - - -
93A GLY* 3.5 23.3 - - - -
94A PHE* 3.4 26.2 - + + -
112A THR* 3.2 28.8 + - - -
113A VAL 3.5 18.2 - - - -
114A ASN* 2.9 25.3 + - - +
118A SER* 5.4 2.2 - - - -
120A GLU* 3.7 42.4 - - + -
121A LEU* 1.3 79.4 - - - +
123A ARG* 1.3 70.5 + - - +
157A TYR* 3.4 12.1 - + + -
218A HIS* 4.3 5.6 - + - -
219A PRO* 3.6 29.2 - - + -
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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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94A PHE* 3.8 4.8 - - - -
112A THR* 4.4 0.2 - - - -
114A ASN* 3.3 23.2 + - - +
121A LEU* 3.6 16.3 - - - +
122A PHE* 1.3 85.6 + - - +
124A TRP* 1.3 66.2 - - - +
125A ASN 3.4 20.4 + - - +
126A VAL* 5.2 0.7 - - - -
128A ASP* 4.2 0.9 - - - +
129A LEU* 3.2 58.4 - - + +
132A LEU* 5.0 7.3 - - - +
156A LEU* 4.3 13.0 - - + -
157A TYR 3.1 6.2 + - - +
158A VAL* 3.2 25.1 - - + +
159A TRP 3.6 0.3 + - - -
187A ASP* 3.4 30.7 - - - +
189A THR* 3.8 15.4 + - - +
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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