Contacts of the strand formed by residues 132 - 143 (chain A) in PDB entry 1VE3
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LYS* 3.6 13.5 + - - +
104A PHE 3.7 13.5 - - - +
106A TYR 4.0 8.7 - - - +
107A VAL* 3.4 26.5 - - + -
128A VAL* 3.1 20.9 + - + +
129A ARG 3.3 14.5 - - - +
130A ARG 3.2 1.3 - - - +
131A VAL* 1.3 77.8 - - - +
133A LYS* 1.3 71.6 + - - +
134A PRO* 3.6 1.7 - - - +
137A LYS 3.8 18.2 - - - +
138A PHE* 3.7 34.5 - - + +
207A PHE* 4.5 2.0 - - + -
226A PRO* 3.8 24.8 - - + +
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Residues in contact with LYS 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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41A LYS* 5.7 1.2 - - - +
102A LYS* 3.5 25.8 - - + +
103A THR 4.1 16.4 - - - -
104A PHE 2.8 19.4 + - - +
105A ASP* 3.3 33.5 + - - +
131A VAL 3.9 0.2 + - - -
132A LEU* 1.3 74.3 - - - +
134A PRO* 1.3 65.7 - - + +
135A SER* 4.1 13.5 - - - +
136A GLY* 2.5 30.0 + - - +
226A PRO* 3.5 6.2 - - - +
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Residues in contact with PRO 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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102A LYS* 3.7 33.7 - - + -
132A LEU 3.6 1.0 - - - +
133A LYS* 1.3 85.6 - - + +
135A SER* 1.3 60.4 + - - +
136A GLY 3.2 0.9 + - - +
225A ASN* 5.5 2.6 - - - +
226A PRO* 3.6 26.5 - - + +
227A LYS 6.2 0.7 - - - +
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Residues in contact with SER 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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105A ASP* 4.9 4.4 + - - -
133A LYS* 2.9 14.8 + - - +
134A PRO* 1.3 79.1 - - - +
136A GLY* 1.3 65.7 + - - +
137A LYS* 4.6 6.4 - - - +
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Residues in contact with GLY 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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104A PHE 4.4 0.2 - - - -
105A ASP* 3.1 24.5 - - - -
132A LEU* 4.1 8.5 - - - -
133A LYS* 2.5 24.2 + - - +
134A PRO 4.3 0.5 - - - +
135A SER* 1.3 77.5 + - - +
137A LYS* 1.3 67.5 + - - +
225A ASN* 3.8 5.2 + - - -
226A PRO* 3.4 16.5 - - - +
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Residues in contact with LYS 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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35A TYR* 2.7 32.2 + - - +
105A ASP 2.8 9.9 + - - +
106A TYR* 3.3 33.0 + - + +
107A VAL 3.1 23.7 + - - +
132A LEU* 3.8 7.0 - - - +
135A SER 4.6 5.6 - - - +
136A GLY* 1.3 79.8 - - - +
138A PHE* 1.3 60.7 + - - +
139A ILE* 3.9 3.6 + - + +
210A GLU* 3.0 34.1 + - - +
223A VAL* 3.8 14.6 - - + -
224A TYR 3.4 5.2 - - - +
225A ASN* 3.5 13.2 - - - +
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Residues in contact with PHE 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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107A VAL* 3.4 17.3 - - + -
109A PHE* 3.7 28.9 - + + -
125A PHE* 3.6 38.8 - + - -
128A VAL* 3.5 26.2 - - + -
132A LEU* 3.7 8.8 - - + +
137A LYS* 1.3 71.4 - - - +
139A ILE* 1.3 59.5 + - - +
140A MSE 4.1 21.1 - - + -
207A PHE* 3.5 34.3 - + + -
222A THR 3.6 1.4 - - - +
223A VAL* 3.6 1.6 - - - -
224A TYR* 2.7 66.7 + + + +
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Residues in contact with ILE 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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32A LEU* 3.8 16.8 - - + +
35A TYR* 4.3 19.7 - - + +
36A MSE 3.7 35.2 - - + -
106A TYR* 4.3 11.2 - - + -
107A VAL 2.9 12.2 + - - +
108A ILE* 3.2 12.2 - - + +
109A PHE 3.0 22.2 + - - -
110A ILE* 5.2 2.1 - - + +
137A LYS* 4.6 6.7 - - + +
138A PHE* 1.3 78.6 - - - +
140A MSE 1.3 62.6 + - - +
221A LEU* 3.8 28.0 - - + -
222A THR 3.4 5.6 - - - +
223A VAL* 4.2 18.2 - - + -
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Residues in contact with MSE 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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109A PHE* 3.1 29.4 - - + +
110A ILE* 5.5 0.4 - - - -
113A ILE* 3.3 32.5 - - + -
125A PHE* 3.8 33.7 - - - -
138A PHE* 4.1 13.5 - - + -
139A ILE* 1.3 75.5 - - - +
141A TYR* 1.3 62.8 + - - +
142A PHE* 3.3 39.9 - - + -
199A VAL* 4.1 12.1 - - + -
220A TYR 3.6 1.2 - - - +
221A LEU* 3.4 4.9 - - - +
222A THR* 2.9 35.6 + - - -
224A TYR* 4.9 12.3 - - + -
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Residues in contact with TYR 141 (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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27A THR* 6.0 0.6 - - + +
28A LEU* 3.8 32.3 - - + -
109A PHE 3.0 8.1 + - - +
110A ILE* 4.1 14.3 - - + +
111A ASP* 3.0 58.4 + - - -
112A SER 4.7 1.0 + - - -
140A MSE 1.3 77.4 - - - +
142A PHE* 1.3 63.9 + - - +
143A THR* 4.4 4.4 + - - -
215A VAL* 3.8 27.6 - - + +
219A SER* 3.1 39.0 + - - -
220A TYR 3.2 18.6 - - - -
221A LEU* 4.1 13.7 - - + -
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Residues in contact with PHE 142 (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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111A ASP* 5.0 4.9 - - - +
113A ILE* 3.4 28.9 - - + -
140A MSE 3.3 35.2 - - + -
141A TYR* 1.3 80.4 - - - +
143A THR* 1.3 69.4 + - - +
144A ASP* 4.2 2.9 + - - -
194A TRP* 5.4 0.4 - - + -
195A GLY 4.6 0.4 - - - -
196A LYS* 3.8 36.8 - - + -
199A VAL* 3.7 31.6 - - + -
200A GLU* 4.8 3.6 - - - -
219A SER* 3.4 3.7 - - - -
220A TYR* 3.0 55.3 + + + -
222A THR* 4.1 13.5 - - - -
224A TYR* 6.1 1.6 - + - -
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Residues in contact with THR 143 (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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111A ASP* 4.3 12.4 + - - -
113A ILE* 4.1 9.8 - - - +
141A TYR* 4.4 2.1 + - - -
142A PHE* 1.3 83.5 - - - +
144A ASP* 1.3 64.6 + - - +
145A LEU* 2.8 22.7 + - + +
148A LEU* 4.1 24.7 - - + -
194A TRP* 3.9 3.5 - - - +
218A TYR* 3.8 8.7 - - + +
219A SER* 3.0 21.4 + - - +
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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