Contacts of the strand formed by residues 132 - 140 (chain A) in PDB entry 4N1T
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 LYS 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A HIS* 6.3 0.2 - - - +
66A LYS* 3.8 19.8 + - - +
67A VAL* 3.1 18.9 - - + +
130A LYS 4.2 6.0 + - - +
131A LYS* 1.3 75.0 - - - +
133A PHE* 1.3 63.4 + - - +
152A GLU* 3.2 10.6 - - - +
153A VAL* 2.9 37.8 + - + +
154A ASP 3.6 24.5 - - - +
155A THR* 5.6 0.2 - - - +
156A VAL* 3.8 20.0 - - + +
202A SO4 5.3 11.5 + - - -
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Residues in contact with PHE 133 (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* 3.1 17.6 + - + -
68A GLY* 3.1 17.9 - - - -
69A GLN 3.1 24.2 + - - -
70A ILE* 3.6 32.5 - - + -
85A VAL* 4.5 8.5 - - + -
123A TRP* 3.5 40.2 - + + -
126A LEU* 4.1 21.5 - - + -
127A LEU* 4.5 9.4 - - + -
131A LYS 3.9 10.5 - - - -
132A LYS* 1.3 79.5 - - - +
134A HIS* 1.3 69.0 + - - +
150A LEU* 3.9 24.0 - - + -
151A ARG 3.2 12.8 - - - +
153A VAL* 3.9 4.7 - - - +
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Residues in contact with HIS 134 (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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69A GLN* 3.3 25.3 + - + +
133A PHE* 1.3 84.0 - - - +
135A GLY* 1.3 59.4 + - - +
149A THR* 4.7 0.5 + - - -
150A LEU* 3.5 3.9 - - - +
151A ARG* 2.9 55.5 + - + +
153A VAL* 3.8 14.3 - - + +
155A THR 3.9 9.1 + - - -
156A VAL* 2.7 34.3 + - - -
205A SO4 4.1 11.9 - - - -
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Residues in contact with GLY 135 (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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69A GLN 2.8 11.1 + - - +
70A ILE* 3.3 11.8 - - - -
71A VAL* 2.9 26.6 + - - +
133A PHE* 4.5 0.8 - - - -
134A HIS* 1.3 75.0 - - - +
136A TYR* 1.3 61.8 + - - +
137A PHE* 4.5 2.5 - - - -
149A THR* 3.3 11.0 - - - -
150A LEU* 3.8 12.3 - - - +
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Residues in contact with TYR 136 (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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71A VAL* 3.3 31.4 - - + -
73A GLU* 2.2 47.2 + - + -
80A LEU* 5.5 2.9 - - + -
135A GLY* 1.3 73.9 - - - +
137A PHE* 1.3 67.0 + - - +
138A LYS* 3.6 33.7 - - + +
147A ASP* 4.6 6.7 - - + -
148A TYR* 3.1 9.3 - - - +
149A THR* 2.9 54.0 + - + +
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Residues in contact with PHE 137 (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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70A ILE* 3.5 27.6 - - + -
71A VAL 2.9 7.5 + - - +
72A PHE* 3.5 12.6 - + + -
73A GLU* 3.0 25.5 + - - +
119A ASP* 3.7 28.7 - - + -
122A TYR* 3.9 29.8 - + + -
123A TRP* 4.2 9.9 - + - -
135A GLY* 4.5 6.1 - - - -
136A TYR* 1.3 86.6 - - - +
138A LYS* 1.3 59.8 + - - +
139A PHE* 3.8 20.0 + - + -
145A ILE* 3.9 14.1 - - + -
147A ASP 3.7 2.7 - - - -
148A TYR* 3.4 37.2 - + + -
149A THR 4.8 0.7 - - - -
150A LEU* 4.8 8.3 - - + -
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Residues in contact with LYS 138 (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 GLU* 3.5 25.0 + - + +
75A VAL* 4.0 17.0 - - + -
136A TYR* 3.6 25.9 - - + +
137A PHE* 1.3 71.6 - - - +
139A PHE* 1.3 57.1 + - - +
145A ILE* 3.5 4.2 - - - -
146A LEU* 2.8 42.2 + - + -
147A ASP* 2.9 38.5 + - + +
203A SO4 3.1 34.8 + - - +
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Residues in contact with PHE 139 (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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72A PHE* 4.0 2.2 - + - -
73A GLU 2.8 10.6 + - - +
74A PHE* 3.5 21.5 - + + -
75A VAL* 3.0 30.1 + - - +
117A TRP* 4.1 4.3 - + - -
118A PRO* 3.7 18.8 - - + -
119A ASP* 3.3 24.5 - - - -
137A PHE* 3.8 27.8 - - + -
138A LYS* 1.3 79.1 - - - +
140A GLN* 1.3 58.9 + - - +
141A GLY 3.4 22.0 - - - +
142A GLN 3.6 22.4 - - - -
144A THR 3.3 12.8 - - - -
145A ILE* 3.7 17.5 - - + -
146A LEU* 4.4 4.0 - - - -
201A 2GD 3.7 20.2 - - - -
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Residues in contact with GLN 140 (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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75A VAL* 3.8 19.5 - - + +
139A PHE* 1.3 70.0 - - - +
141A GLY* 1.3 66.5 + - - +
142A GLN 3.7 0.2 + - - -
143A ASP 4.1 0.7 + - - -
144A THR* 2.9 33.7 + - + +
146A LEU* 3.8 37.4 - - + +
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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