Contacts of the strand formed by residues 127 - 134 (chain D) in PDB entry 1VEW
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 GLY 127 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ARG* 3.9 6.6 - - - +
125D GLY 3.9 1.2 + - - -
126D SER* 1.3 77.2 - - - +
128D TRP* 1.3 66.3 + - - -
143D THR 3.3 12.8 - - - -
145D ASN 3.7 11.4 - - - -
168D VAL* 2.9 30.5 + - - +
169D TRP* 3.3 15.3 - - - +
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Residues in contact with TRP 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.5 44.8 - - + +
81D HIS* 3.7 18.2 - + - -
83D LEU* 6.1 0.4 - - + -
84D PHE* 3.8 27.1 - + + -
123D ARG* 4.4 1.4 - - - +
127D GLY* 1.3 75.0 - - - -
129D ALA* 1.3 61.0 + - - +
130D TRP* 3.5 37.2 - + + +
142D SER* 3.2 6.3 - - - -
143D THR* 2.9 34.3 + - - +
145D ASN 3.3 21.9 + - - -
146D GLN* 3.0 19.4 + - - -
147D ASP 4.6 0.2 - - - -
165D GLY 4.5 2.2 - - - -
166D LEU 3.3 14.6 - - - -
167D ASP* 3.5 53.3 + - + -
168D VAL* 4.0 5.6 - - - +
169D TRP* 4.0 0.2 - - - +
207D OH 4.0 0.4 + - - -
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 3.8 18.8 - - + +
119D ALA* 4.4 6.3 - - + -
120D ALA* 3.8 39.9 - - + +
128D TRP* 1.3 75.4 - - - +
130D TRP* 1.3 63.4 + - - +
141D VAL 3.6 6.3 - - - +
142D SER* 4.2 2.2 - - - +
165D GLY* 3.2 3.5 - - - -
166D LEU* 2.8 33.5 + - + +
168D VAL* 4.8 1.9 - - + +
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Residues in contact with TRP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.3 35.2 - - + -
83D LEU* 4.2 21.1 - - + -
116D PHE* 3.8 7.8 - - - -
128D TRP* 3.5 36.2 - + + +
129D ALA* 1.3 76.8 - - - +
131D LEU* 1.3 59.6 + - - +
132D VAL* 3.8 17.0 + - + -
139D ALA 3.7 0.3 - - - +
140D VAL* 3.3 8.1 - - - +
141D VAL* 2.7 50.4 + - + +
142D SER* 4.1 0.4 - - - -
143D THR* 2.9 27.6 + - + -
147D ASP 3.9 7.6 - - - -
148D SER* 4.9 1.3 - - - -
149D PRO* 3.5 25.4 - - + +
162D PRO* 4.0 19.1 - - + -
164D MET 3.5 8.3 - - - +
165D GLY* 3.7 23.8 - - - -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 5.0 3.1 - - + -
102D ILE* 4.6 14.4 - - + -
106D PHE* 4.3 5.2 - - + -
112D PHE* 3.9 27.1 - - + -
116D PHE* 4.0 2.3 - - + -
130D TRP* 1.3 71.1 - - - +
132D VAL* 1.3 60.1 + - - +
138D LEU* 4.1 22.0 - - + -
139D ALA 3.4 27.6 - - - +
140D VAL* 4.5 1.3 - - + +
162D PRO* 3.8 0.7 - - - +
163D ILE* 2.8 46.6 + - + +
164D MET* 2.9 43.9 + - + +
194D TRP* 5.4 2.0 - - + -
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D TRP* 3.8 20.6 - - + -
131D LEU* 1.3 78.0 - - - +
133D LEU* 1.3 60.9 + - - +
134D LYS* 3.7 17.3 - - + -
138D LEU* 3.3 10.1 - - - +
139D ALA* 2.7 52.1 + - + +
141D VAL* 3.9 13.0 - - + -
149D PRO* 3.9 24.0 - - + -
159D SER 3.6 17.3 - - - +
160D GLY 4.1 3.8 - - - -
161D PHE 3.2 13.2 - - - +
162D PRO* 4.1 4.5 - - + -
163D ILE* 4.4 0.9 - - - -
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D VAL* 1.3 71.1 - - - +
134D LYS* 1.3 59.1 + - - +
135D GLY 3.7 17.2 + - - +
136D ASP* 3.7 23.6 - - - +
137D LYS 3.5 17.7 - - - +
138D LEU* 4.0 15.9 - - + -
160D GLY* 3.6 1.4 - - - -
161D PHE* 2.8 39.7 + - + +
163D ILE* 4.2 11.4 - - + -
201D PHE* 4.5 20.2 - - + +
204D LYS* 3.7 42.4 - - + +
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Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D VAL* 3.7 17.0 - - + -
133D LEU* 1.3 70.3 - - - +
135D GLY* 1.3 59.3 + - - +
136D ASP* 3.0 10.1 + - - +
137D LYS* 2.7 24.9 + - + +
139D ALA* 4.2 14.4 - - + -
141D VAL* 5.2 8.0 - - + +
153D GLU* 4.8 7.5 + - - -
159D SER* 3.6 44.1 + - - +
160D GLY* 3.9 5.2 - - - -
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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