Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 2AOQ
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 VAL 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.7 0.2 - - - -
77A GLU* 3.3 11.9 - - + +
79A LYS* 4.0 19.1 - - + -
116A LYS 3.8 17.9 - - - +
117A LEU* 4.0 14.4 - - + -
119A CYS* 1.3 78.4 - - - +
121A LEU* 1.3 64.5 + - - +
122A TRP* 3.6 37.6 + - + +
142A ILE 3.7 1.2 - - - +
143A PHE* 3.7 5.6 - - - -
144A TRP* 2.8 62.8 + - + +
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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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17A LEU* 3.9 35.9 - - + -
18A LEU* 4.5 13.0 - - + -
21A ALA* 4.7 7.2 - - + -
59A LEU* 4.4 7.0 - - + -
71A PHE* 5.1 0.9 - - + -
76A VAL* 3.9 16.3 - - + +
77A GLU 2.8 10.5 + - - +
78A LEU* 3.5 27.1 - - + +
79A LYS 3.1 21.5 + - - +
120A VAL* 1.3 74.5 - - - +
122A TRP* 1.3 73.3 + - - +
123A MET* 4.2 2.7 - - - -
141A PRO* 3.7 23.1 - - + -
142A ILE 3.7 9.6 - - - +
143A PHE* 4.5 5.2 - - + -
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Residues in contact with TRP 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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79A LYS* 3.3 31.0 - - + -
80A THR 4.8 0.9 - - - -
81A LEU* 4.2 28.0 - - + -
93A THR* 3.8 29.4 - - + -
117A LEU* 4.8 1.3 - - + -
120A VAL* 3.6 18.2 - - + +
121A LEU* 1.3 76.4 - - - +
123A MET* 1.3 59.6 + - - +
124A PRO* 3.4 7.6 - - + +
141A PRO* 3.7 0.5 - - - +
142A ILE* 2.9 46.9 + - + +
144A TRP* 3.5 52.5 - + + +
213A LEU* 3.9 25.8 - - + -
218A THR* 3.9 9.4 - - + -
221A ILE* 3.8 31.4 - - + +
222A LEU* 6.2 0.2 - - + -
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Residues in contact with MET 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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21A ALA* 3.9 17.0 - - + +
24A ILE* 3.8 20.9 - - + -
55A LEU* 3.7 38.6 - - + -
59A LEU* 4.4 0.9 - - + -
78A LEU* 3.8 23.1 - - + -
79A LYS 2.9 12.9 + - - +
80A THR* 3.3 6.3 - - + -
81A LEU* 3.1 18.7 + - - -
121A LEU* 4.2 4.3 - - + +
122A TRP* 1.3 73.2 - - - +
124A PRO* 1.3 68.9 - - - +
125A ILE* 3.5 5.9 + - + +
138A ILE* 3.8 6.1 - - + -
139A GLY 3.8 18.2 - - - +
141A PRO* 3.6 30.5 - - + -
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Residues in contact with PRO 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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81A LEU* 3.4 17.7 - - + +
83A ILE* 4.2 19.5 - - + -
122A TRP* 3.4 9.0 - - + +
123A MET* 1.3 86.3 - - - +
125A ILE* 1.3 56.1 + - - +
138A ILE* 4.5 0.5 - - - +
139A GLY* 2.7 37.3 + - - -
140A ALA 3.2 25.4 - - - +
142A ILE* 3.9 23.6 - - + -
222A LEU* 4.1 13.7 - - + -
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Residues in contact with ILE 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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29A PHE* 3.9 21.5 - - + -
44A LEU* 6.3 0.2 - - + -
51A VAL* 3.4 41.5 - - + -
55A LEU* 4.9 3.4 - - + -
80A THR* 4.2 15.9 - - + -
81A LEU 3.0 6.7 + - - +
82A PRO* 3.8 15.7 - - + -
83A ILE* 2.9 30.5 + - - +
123A MET* 3.6 9.4 - - + +
124A PRO* 1.3 81.2 - - - +
126A GLU* 1.3 66.1 + - - +
127A GLY* 5.6 0.2 - - - -
137A HIS 3.6 5.4 - - - +
138A ILE* 4.4 12.6 - - + -
139A GLY 4.3 0.7 - - - +
7C T 4.3 14.8 - - - +
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Residues in contact with GLU 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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29A PHE* 4.0 6.9 - - - -
83A ILE* 3.8 11.7 - - + +
84A ASN 6.2 1.3 - - - +
125A ILE* 1.3 74.2 - - - +
127A GLY* 1.3 59.7 + - - +
128A SER 3.8 0.9 - - - +
131A ILE* 3.6 23.2 - - + +
135A GLU 4.0 1.4 - - - +
136A ARG* 3.4 31.0 + - + +
137A HIS* 2.8 66.0 + - + +
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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