Contacts of the strand formed by residues 133 - 143 (chain B) in PDB entry 5YVT
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLU* 1.3 75.4 - - - +
134B GLU* 1.3 58.7 + - - -
136B SER* 2.7 29.5 + - - -
137B SER 3.5 2.8 + - - -
151B LYS* 3.9 12.3 - - - +
152B ILE 3.0 20.2 + - - -
153B ILE* 4.1 7.3 - - - +
235B ASN* 3.7 9.6 - - - -
236B LEU* 4.1 12.6 - - - -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LYS* 4.8 0.5 - - - +
176A ILE* 3.4 31.4 - - + +
177A MET* 5.4 4.3 - - - +
228A TYR* 2.7 40.4 + - + -
90B LYS* 5.6 0.9 + - - -
132B GLU 3.2 0.6 + - - -
133B GLY* 1.3 71.2 - - - -
135B TYR* 1.3 65.7 + - + +
137B SER* 3.2 23.1 - - - -
151B LYS* 4.3 19.3 - - + -
235B ASN* 2.9 30.4 + - - +
236B LEU* 3.4 12.3 + - + +
238B GLY* 3.4 23.6 + - - -
239B ASN 4.5 1.7 + - - -
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Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 4.0 12.8 - - + -
90B LYS* 3.9 17.3 + - - +
94B ASN* 3.2 44.0 + - + -
97B ARG* 2.7 34.1 + - + -
98B THR* 4.1 19.6 - - + +
128B ARG* 2.9 10.0 + - - -
130B ASN* 3.1 38.6 - - - -
131B THR* 3.9 12.1 - - - +
132B GLU 3.1 7.2 + - - +
134B GLU* 1.3 79.8 - - + +
136B SER* 1.3 57.4 + - - +
137B SER 3.3 1.7 + - - -
235B ASN* 3.1 25.1 + - - -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS* 5.4 0.4 - - - -
131B THR 4.9 2.5 - - - -
132B GLU* 4.0 8.7 + - - -
133B GLY 2.7 25.5 + - - -
135B TYR* 1.3 77.6 - - - +
137B SER* 1.3 64.5 + - - +
138B LEU* 3.5 4.7 + - - +
150B LEU 3.7 4.6 - - - +
152B ILE* 3.1 39.0 + - - +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 4.8 4.3 + - - -
177A MET* 3.7 31.7 - - - +
90B LYS* 3.9 17.3 + - - -
133B GLY 3.5 1.9 + - - -
134B GLU* 3.2 20.8 + - - -
135B TYR 3.3 1.2 - - - -
136B SER* 1.3 79.2 + - - +
138B LEU* 1.3 60.5 + - - +
139B GLU* 4.2 9.4 + - - +
149B SER* 4.3 4.9 - - - -
150B LEU 3.5 8.4 + - - -
151B LYS* 4.5 10.3 - - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B SER 4.5 2.7 - - - +
137B SER* 1.3 75.3 + - - +
139B GLU* 1.3 74.3 + - - +
140B HIS* 4.1 22.4 - - + -
148B GLU 3.6 1.4 - - - +
149B SER* 3.3 2.6 - - - -
150B LEU* 2.9 50.5 + - + +
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE 4.2 3.5 - - - +
177A MET* 3.4 13.6 - - - +
178A ARG* 3.2 14.3 + - - +
179A MET* 2.8 56.6 + - + +
180A SER* 2.4 37.9 + - - +
87B PRO* 5.3 0.9 - - - +
137B SER* 4.2 11.6 + - - +
138B LEU* 1.3 86.0 - - - +
140B HIS* 1.3 63.0 + - - +
147B VAL* 4.4 1.6 - - + -
148B GLU 3.3 6.1 - - - +
149B SER* 4.3 8.1 - - - -
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Residues in contact with HIS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A MET* 4.1 7.6 - - - -
138B LEU* 4.1 11.4 - - + -
139B GLU* 1.3 77.0 - - - +
141B GLU* 1.3 59.3 + - - +
142B SER* 2.8 36.1 + - - +
146B VAL 3.7 0.9 - - - +
147B VAL* 3.6 1.4 - - - -
148B GLU* 2.9 69.0 + - + +
150B LEU* 3.6 22.6 - - + +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A MET* 4.1 15.0 - - - +
183A LEU* 5.9 2.4 - - - +
140B HIS* 1.3 72.8 - - - +
142B SER* 1.3 62.0 + - - +
143B VAL 3.3 11.2 + - - +
144B ALA* 3.7 6.3 - - - +
145B GLY* 2.9 25.4 + - - -
146B VAL 3.3 20.6 - - - +
147B VAL* 4.1 17.7 - - + +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B HIS* 2.8 37.1 + - - +
141B GLU* 1.3 74.5 - - - +
143B VAL* 1.3 65.8 + - - +
146B VAL 4.3 1.2 + - - -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU* 3.6 5.6 - - - +
142B SER* 1.3 84.4 - - - +
144B ALA* 1.3 73.8 + - + +
145B GLY 3.3 0.2 + - - -
146B VAL* 3.0 44.0 + - + +
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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