Contacts of the strand formed by residues 133 - 141 (chain B) in PDB entry 5DSV
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 CYS 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.9 4.5 - - - -
78B ALA 3.4 14.8 - - - +
80B LEU 3.8 13.2 - - - +
83B ASP* 4.0 5.8 - - - -
84B ALA* 3.4 29.6 - - + +
87B LEU* 3.3 32.6 - - - +
119B VAL* 5.5 1.0 - - - +
131B PHE* 3.3 8.1 + - - +
132B GLY* 1.3 80.0 - - - +
134B SER* 1.3 62.5 + - - +
135B PHE* 4.5 6.4 - - - -
151B ILE 4.4 0.3 - - - +
152B ASP 4.2 1.9 - - - -
153B PRO* 3.6 19.4 - - - +
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Residues in contact with SER 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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30B VAL* 3.4 19.1 - - - +
77B VAL* 3.7 0.9 - - - +
78B ALA 3.0 29.5 + - - +
133B CYS* 1.3 78.1 - - - +
135B PHE* 1.3 66.7 + - - +
150B MET* 4.4 1.9 - - - -
151B ILE 3.2 10.8 - - - -
152B ASP* 3.5 10.3 - - - +
153B PRO* 3.5 17.3 - - - +
165B ILE* 4.0 25.2 - - - +
169B ARG* 4.1 7.8 + - - -
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Residues in contact with PHE 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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75B MET* 3.7 26.7 - - + -
76B ALA 3.1 13.7 - - - +
77B VAL* 3.7 16.8 - - + -
87B LEU* 4.0 27.1 - - + -
91B ALA* 6.1 0.4 - - + -
115B VAL* 3.5 31.0 - - + -
119B VAL* 4.3 3.1 - - + -
133B CYS* 4.5 3.4 - - - -
134B SER* 1.3 82.3 - - - +
136B MET* 1.3 65.6 + - - +
137B LEU* 4.0 19.5 - - + -
150B MET* 3.3 4.7 - - - +
151B ILE* 2.8 79.4 + - + +
165B ILE* 4.0 3.1 - - - -
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Residues in contact with MET 136 (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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37B ILE* 4.2 8.3 - - - -
38B GLY* 4.0 21.8 - - - +
47B PHE* 3.8 21.0 - - + -
74B GLY 3.5 0.7 - - - +
75B MET* 3.2 6.4 - - - +
76B ALA* 2.8 40.5 + - - +
135B PHE* 1.3 79.6 - - - +
137B LEU* 1.3 62.5 + - - +
148B LEU* 4.2 10.5 - - + -
149B TYR 2.9 12.8 - - - +
150B MET* 4.0 13.9 - - + -
163B CYS* 3.4 50.9 - - + +
164B ALA 4.0 1.3 - - - +
165B ILE* 4.0 17.3 - - + -
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Residues in contact with LEU 137 (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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47B PHE* 3.9 2.7 - - - -
69B VAL* 4.5 4.0 - - + -
73B VAL* 4.3 10.3 - - + -
74B GLY 3.2 4.7 - - - +
75B MET* 3.8 35.0 - - + -
91B ALA* 5.2 2.7 - - + -
108B LEU* 3.5 18.6 - - + +
111B LEU* 4.3 16.4 - - + +
112B ALA* 3.9 35.2 - - + +
115B VAL* 5.4 4.5 - - + -
135B PHE* 4.0 21.5 - - + -
136B MET* 1.3 74.3 - - - +
138B GLY* 1.3 57.7 - - - +
148B LEU* 3.4 3.6 - - - +
149B TYR* 2.8 36.5 + - + +
151B ILE* 4.4 4.0 - - + -
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Residues in contact with GLY 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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45B VAL* 4.6 4.3 - - - -
47B PHE* 3.6 18.8 - - - -
72B HIS 3.9 0.3 - - - +
73B VAL* 3.4 0.9 - - - -
74B GLY* 2.9 33.4 + - - -
108B LEU* 3.9 2.0 - - - -
137B LEU* 1.3 74.9 - - - +
139B SER* 1.3 62.7 + - - -
147B GLN 3.3 9.4 - - - -
148B LEU* 4.5 2.5 - - - -
216B VAL* 4.1 9.8 - - - +
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Residues in contact with SER 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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45B VAL* 3.9 2.6 - - - +
72B HIS* 3.1 35.3 - - - -
108B LEU* 3.6 31.9 + - - +
138B GLY* 1.3 74.1 - - - -
140B TYR* 1.3 63.1 + - - +
141B SER 4.7 0.9 + - - -
144B ASP* 6.1 0.5 - - - +
145B GLY 3.9 1.0 + - - +
146B ALA* 3.6 2.3 - - - -
147B GLN* 2.9 40.3 + - - +
216B VAL* 3.8 10.0 - - - +
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Residues in contact with TYR 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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42B LYS 4.7 3.1 - - - -
43B ASP* 3.6 22.6 - - - -
44B GLY* 4.4 2.0 - - - -
72B HIS* 4.4 8.8 - - - +
139B SER* 1.3 76.7 - - - +
141B SER* 1.3 83.8 + - - +
142B VAL* 3.9 23.5 + - + +
145B GLY* 3.5 14.6 - - - -
146B ALA* 3.5 23.8 - - + -
216B VAL* 3.7 8.4 - - + +
217B GLY* 3.5 22.2 - - - +
218B GLU* 3.2 45.8 + - + +
221B ASN 5.5 0.7 - - - -
222B GLY* 3.4 28.0 - - - +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B HIS* 5.8 4.5 - - - -
105B ASN* 5.7 7.2 - - - -
139B SER* 4.7 1.8 + - - -
140B TYR* 1.3 86.9 - - - +
142B VAL* 1.3 62.1 + - - +
143B ASN* 3.7 5.4 + - - +
144B ASP* 3.5 28.8 + - - +
145B GLY* 2.9 31.1 + - - +
222B GLY* 5.2 2.5 - - - -
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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