Contacts of the strand formed by residues 121 - 131 (chain A) in PDB entry 3WUZ
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 SER 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ARG* 3.5 28.5 + - - -
74A GLY 3.1 29.2 + - - -
75A HIS* 5.4 1.9 - - - +
119A ASP 3.2 3.0 + - - -
120A GLN* 1.3 76.2 - - - +
122A VAL* 1.3 68.9 + - - +
123A TYR* 3.7 17.5 - - - -
146A LYS* 3.6 4.0 - - - +
147A LEU 2.8 28.8 + - - +
202A CIT 4.1 2.1 + - - -
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Residues in contact with VAL 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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73A ARG* 3.1 5.2 - - - -
74A GLY 2.9 38.2 + - - +
75A HIS* 5.4 5.2 - - + -
121A SER* 1.3 80.5 + - - +
123A TYR* 1.3 60.8 + - - +
124A PHE* 3.5 22.7 - - + -
143A GLU 3.3 26.7 - - - +
145A THR 3.4 14.4 - - - +
146A LYS* 4.2 25.6 - - + +
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Residues in contact with TYR 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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37A GLN* 3.0 9.5 + - - -
51A ILE* 3.8 22.2 - - + -
71A TRP* 4.4 7.6 - + + -
72A ARG 3.3 4.3 - - - -
73A ARG* 4.0 5.0 + - + -
81A PHE* 3.5 39.5 - + - -
93A TYR* 2.8 26.4 + - - -
112A ILE* 3.7 18.5 - - + +
119A ASP* 2.6 37.6 + - - +
121A SER* 3.7 23.8 - - - -
122A VAL* 1.3 74.1 - - - +
124A PHE* 1.3 61.7 + - - +
144A GLY* 3.2 1.7 - - - -
145A THR* 2.8 34.9 + - - +
147A LEU* 3.8 21.5 - - + -
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Residues in contact with PHE 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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37A GLN* 3.7 3.6 - - - +
70A SER 3.7 0.3 - - - +
71A TRP* 3.2 11.0 - - - -
72A ARG* 2.8 52.6 + - + +
73A ARG 4.8 0.4 - - - -
74A GLY* 4.5 10.3 - - - -
78A GLY* 6.0 2.5 - - - -
122A VAL* 3.5 41.3 - - + -
123A TYR* 1.3 76.0 - - - +
125A CYS* 1.3 58.3 + - - +
126A ARG 4.0 0.5 + - - -
140A GLN* 4.1 26.0 - - + +
141A SER* 3.3 18.8 - - - -
142A ILE 3.5 23.1 - - - -
143A GLU* 3.6 11.7 - - - -
144A GLY* 3.8 7.2 - - - -
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Residues in contact with CYS 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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35A VAL* 3.8 12.4 - - + +
37A GLN* 2.8 20.1 + - - +
53A PHE* 4.0 22.9 - - + -
69A ILE* 3.9 19.3 - - - -
70A SER 3.6 3.4 - - - -
71A TRP* 3.6 33.6 - - + -
124A PHE* 1.3 73.1 - - - +
126A ARG* 1.3 63.7 + - - +
127A VAL* 4.2 9.6 - - - -
140A GLN* 3.3 3.4 - - - +
141A SER 3.0 25.3 + - - -
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Residues in contact with ARG 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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68A ARG 3.7 1.1 - - - +
69A ILE* 3.3 8.0 - - - +
70A SER* 2.8 55.1 + - - +
72A ARG* 3.5 34.6 - - - +
80A SER* 5.4 1.6 + - - -
124A PHE 4.0 0.4 + - - -
125A CYS* 1.3 72.8 - - - +
127A VAL* 1.3 65.5 + - - +
128A GLU* 5.1 3.1 - - + +
138A GLN* 3.6 43.7 + - + +
139A TRP 3.3 12.1 - - - +
140A GLN* 2.7 35.3 + - + +
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Residues in contact with VAL 127 (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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35A VAL* 3.7 20.6 - - + -
53A PHE* 5.0 2.7 - - + -
55A PHE* 3.9 28.0 - - + -
67A VAL* 4.4 7.9 - - + -
68A ARG 3.7 3.1 - - - -
69A ILE* 4.2 17.9 - - + -
125A CYS* 4.2 7.4 - - - -
126A ARG* 1.3 75.8 - - - +
128A GLU* 1.3 62.4 + - - +
129A LEU* 3.9 28.0 - - + -
138A GLN* 3.3 4.3 - - - -
139A TRP* 2.8 40.0 + - - +
201A IPA 4.0 10.5 - - - +
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Residues in contact with GLU 128 (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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67A VAL* 3.3 1.7 - - - +
68A ARG* 2.8 55.5 + - + +
126A ARG* 4.2 3.5 - - + -
127A VAL* 1.3 75.3 - - - +
129A LEU* 1.3 66.9 + - - +
136A ARG* 2.9 40.8 + - + +
137A GLN 3.2 14.8 - - - +
138A GLN* 3.0 28.3 - - + +
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Residues in contact with LEU 129 (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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55A PHE* 4.0 9.4 - - + -
61A LEU* 3.8 22.0 - - + -
65A PRO* 3.4 14.6 - - + +
67A VAL* 3.9 11.7 - - + -
127A VAL* 3.9 15.3 - - + -
128A GLU* 1.3 77.7 - - - +
130A ASP* 1.3 74.0 + - - +
131A THR* 3.7 3.3 + - + -
136A ARG* 3.4 10.1 - - - +
137A GLN* 2.9 31.7 + - - +
139A TRP* 3.6 24.7 - - + -
201A IPA 3.9 34.3 - - + -
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Residues in contact with ASP 130 (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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61A LEU* 3.8 4.3 - - - +
62A ALA* 2.9 36.4 + - + +
64A ALA 3.8 7.0 - - - +
65A PRO* 2.8 18.6 + - - +
66A ASP* 4.6 3.1 - - - +
129A LEU* 1.3 79.6 - - - +
131A THR* 1.3 61.9 + - - +
135A GLY* 3.8 5.7 - - - -
136A ARG* 2.7 53.4 + - - +
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Residues in contact with THR 131 (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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57A TYR* 3.8 34.1 - - + +
60A GLU 3.9 6.7 - - - -
61A LEU* 4.1 1.8 - - - +
62A ALA* 3.6 9.3 - - - +
129A LEU* 3.9 15.7 - - + -
130A ASP* 1.3 78.4 - - - +
132A ARG* 1.3 66.4 + - - +
133A SER 4.3 0.9 - - - -
134A SER* 2.9 24.8 + - - -
135A GLY* 2.8 30.7 + - - +
137A GLN* 4.0 15.7 - - + -
139A TRP* 4.0 2.9 - - + -
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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