Contacts of the strand formed by residues 122 - 132 (chain A) in PDB entry 3N2Q
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 LEU 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ALA* 3.8 2.1 - - - +
113A LEU* 3.5 26.5 - - + +
114A VAL* 3.8 25.1 - - + +
120A PRO* 3.7 18.0 - - - +
121A VAL* 1.3 79.2 - - - +
123A THR* 1.3 59.4 + - - +
124A ASN 3.4 22.2 - - - +
125A ILE* 3.8 13.2 - - + -
148A LEU* 4.0 26.9 - - + -
149A ALA 3.3 9.9 - - - +
150A MSE 3.9 13.4 - - + -
162A LYS* 4.4 5.9 - - + +
166A VAL* 3.8 26.0 - - + -
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Residues in contact with THR 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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64A ILE* 4.1 5.2 - - - +
67A ALA* 3.6 28.2 - - + +
68A ASN* 3.1 21.7 + - - +
71A THR* 4.1 3.8 - - + +
114A VAL* 3.4 14.0 - - - +
120A PRO* 5.3 0.2 - - + -
121A VAL 3.6 12.1 - - - +
122A LEU* 1.3 78.8 - - - +
124A ASN* 1.3 75.7 + - - +
149A ALA* 2.8 14.7 + - - +
151A SER* 3.9 12.6 - - - -
192A GLN* 2.5 33.1 + - - +
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Residues in contact with ASN 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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62A LYS 4.8 1.2 - - - +
63A VAL* 3.8 9.1 - - - +
64A ILE* 3.0 46.2 + - - +
68A ASN* 4.0 4.9 - - - +
75A LEU* 3.7 25.1 - - - +
80A TYR* 3.1 21.7 - - + +
110A ILE* 5.8 0.9 - - - +
114A VAL* 4.0 8.1 - - - +
122A LEU* 3.4 9.9 - - - +
123A THR* 1.3 88.9 + - - +
125A ILE* 1.3 66.7 + - - +
126A ILE* 5.2 0.9 - - + -
147A GLY 3.7 0.5 - - - +
149A ALA* 3.0 29.4 + - + +
192A GLN* 5.7 0.4 - - - +
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Residues in contact with ILE 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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61A GLN* 5.5 0.7 - - - +
62A LYS 5.1 6.2 - - - +
102A ASN* 4.9 3.6 + - - -
105A ILE* 4.1 20.4 - - + -
110A ILE* 4.1 38.8 - - + +
113A LEU* 4.3 19.5 - - + -
114A VAL* 3.9 12.6 - - + +
122A LEU* 3.8 23.8 - - + -
124A ASN* 1.3 84.9 + - - +
126A ILE* 1.3 69.1 + - - +
146A ILE* 3.9 23.1 - - + -
147A GLY 3.4 3.6 - - - -
148A LEU* 3.9 10.3 - - + -
166A VAL* 4.6 1.3 - - + -
170A LEU* 4.2 11.7 - - + -
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 3.4 29.2 - - + +
62A LYS 5.8 0.7 - - - +
63A VAL* 4.8 9.4 - - + -
77A LEU* 5.6 0.7 - - + -
80A TYR* 3.4 64.6 - - + +
81A GLU* 4.1 13.0 - - + +
84A LEU* 3.7 20.6 - - + -
102A ASN* 4.3 2.0 - - - -
110A ILE* 6.5 0.2 - - - -
124A ASN* 5.2 0.7 - - + -
125A ILE* 1.3 79.7 - - - +
127A GLU* 1.3 60.3 + - - +
128A GLN* 4.6 4.3 - - + +
146A ILE* 3.2 9.4 - - - +
147A GLY 2.9 36.9 + - - +
203A TYR* 4.2 0.2 - - - +
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Residues in contact with GLU 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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61A GLN* 4.0 1.0 - - - +
101A LEU* 3.4 6.6 - - - +
102A ASN* 2.8 50.4 + - - +
103A GLN 3.2 10.4 + - - -
104A TYR* 2.9 26.4 + - - +
105A ILE* 3.0 48.6 + - + +
110A ILE* 6.2 0.7 - - + -
125A ILE* 5.6 0.2 - - + -
126A ILE* 1.3 76.0 - - - +
128A GLN* 1.3 64.6 + - - +
129A ASP* 2.6 26.1 - - - +
144A VAL* 4.0 14.1 - - + +
145A MSE 3.5 2.7 - - - -
146A ILE* 4.5 1.6 - - + -
174A ILE* 5.5 0.2 - - - -
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Residues in contact with GLN 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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61A GLN* 4.8 4.1 + - - +
81A GLU* 3.4 34.4 + - - +
84A LEU* 3.5 29.3 - - + +
85A ILE* 3.6 19.4 + - - +
99A LEU* 3.7 12.7 - - + +
100A GLN 3.8 3.1 - - - -
101A LEU* 4.0 17.5 - - + +
126A ILE* 4.6 3.8 - - + +
127A GLU* 1.3 77.2 - - - +
129A ASP* 1.3 61.7 + - - +
130A TYR* 3.1 28.0 + - + -
144A VAL* 3.5 2.1 - - - -
145A MSE 2.7 43.2 + - + +
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Residues in contact with ASP 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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98A VAL 3.5 2.8 - - - +
99A LEU* 3.5 2.1 - - - -
100A GLN 2.7 41.0 + - - +
102A ASN 3.3 10.2 + - - -
103A GLN* 2.9 39.0 + - + +
104A TYR* 3.6 7.3 - - - -
127A GLU* 2.6 27.0 - - - +
128A GLN* 1.3 73.0 - - - +
130A TYR* 1.3 61.7 + - - +
131A PHE* 3.6 21.4 - - + -
141A LEU* 4.1 7.2 - - + -
143A GLY 3.9 3.8 - - - -
144A VAL* 3.6 12.3 - - - +
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Residues in contact with TYR 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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85A ILE* 3.6 17.9 - - + +
88A ALA* 3.5 23.0 - - + +
92A PHE* 4.2 18.6 - + + -
94A THR* 4.1 22.4 - - + -
97A HIS* 4.0 22.2 - - + -
98A VAL 3.5 1.8 - - - -
99A LEU* 3.8 24.9 - - + +
128A GLN* 3.1 37.1 + - + -
129A ASP* 1.3 74.8 - - - +
131A PHE* 1.3 57.1 + - - +
141A LEU* 3.3 4.9 - - - +
142A SER* 2.8 32.7 + - - -
143A GLY 3.0 15.8 + - - +
145A MSE 3.5 25.6 - - + -
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Residues in contact with PHE 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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97A HIS* 3.0 6.5 - - - +
98A VAL* 2.7 52.6 + - + +
100A GLN* 3.5 35.7 - - + -
103A GLN* 4.5 8.1 - - + -
104A TYR* 3.9 22.9 - - - -
129A ASP* 3.6 28.7 - - + -
130A TYR* 1.3 75.5 - - - +
132A GLY* 1.3 57.9 + - - +
139A LEU* 3.4 15.6 - - + +
140A SER* 3.0 32.1 - - - +
141A LEU* 3.5 13.7 - - + -
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Residues in contact with GLY 132 (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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96A SER* 4.2 4.9 - - - -
97A HIS* 3.2 19.3 - - - -
131A PHE* 1.3 73.6 - - - +
133A LYS* 1.3 62.2 + - - -
138A GLU 4.0 0.2 - - - +
139A LEU* 3.4 13.2 - - - -
140A SER* 2.8 32.5 + - - +
142A SER* 3.4 11.3 + - - -
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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