Contacts of the strand formed by residues 145 - 151 (chain L) 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 GLY 145 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40L ARG* 6.0 0.4 - - - -
139L SER* 3.9 1.7 + - - +
140L TYR* 3.5 12.1 - - - -
141L SER 2.9 33.6 + - - +
142L VAL 3.6 6.8 + - - -
143L ASN 3.6 2.2 - - - -
144L ASP* 1.3 83.4 - - - +
146L ALA* 1.3 61.6 + - - -
147L GLN* 4.0 4.0 + - - +
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Residues in contact with ALA 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ARG* 3.1 42.4 + - + +
41L CYS 4.3 2.7 - - - +
42L LYS 4.7 5.3 + - - +
44L GLY* 3.4 41.7 - - - +
139L SER 3.6 5.6 - - - -
140L TYR* 3.5 8.2 - - + -
144L ASP 4.5 1.2 - - - +
145L GLY* 1.3 69.3 - - - -
147L GLN* 1.3 69.0 + - - +
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Residues in contact with GLN 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ARG* 4.4 5.8 - - - +
45L VAL* 3.5 6.7 - - - +
107L PRO 5.0 0.2 - - - -
108L LEU* 3.7 38.5 - - + +
109L LYS* 3.6 34.7 - - - +
138L GLY* 3.3 4.7 - - - -
139L SER* 3.0 37.8 + - - +
144L ASP* 3.8 34.9 + - - +
145L GLY 4.0 8.3 - - - +
146L ALA* 1.3 81.4 - - - +
148L LEU* 1.3 60.3 + - - +
149L TYR* 4.0 10.6 + - + -
59M GLU* 5.4 3.8 - - - +
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Residues in contact with LEU 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L GLY 3.7 9.4 - - - +
39L ILE* 3.9 6.5 - - - +
40L ARG* 4.6 6.5 - - + +
45L VAL* 3.9 14.1 - - + -
47L PHE* 3.5 38.1 - - + -
136L MET* 4.2 13.2 - - + -
137L LEU 3.4 7.2 - - - +
147L GLN* 1.3 75.3 - - - +
149L TYR* 1.3 68.1 + - - +
159L GLY* 3.5 4.5 - - - -
160L TYR* 2.9 54.1 + - + +
161L TRP 4.0 2.9 - - - +
162L GLY* 3.7 30.1 - - - -
163L CYS 4.0 2.5 - - - +
59M GLU* 5.4 0.3 - - - +
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Residues in contact with TYR 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L LEU* 3.7 20.2 - - + -
109L LYS* 3.4 48.0 - - - +
112L ALA* 3.9 19.7 - - + -
136L MET* 2.9 9.2 - - - +
137L LEU* 2.8 44.7 + - + +
147L GLN* 4.0 16.3 + - + -
148L LEU* 1.3 81.9 - - - +
150L MET* 1.3 59.8 + - - +
151L ILE* 5.1 2.9 - - + -
157L SER* 3.6 18.8 - - - +
158L TYR* 3.2 18.6 - - - -
159L GLY* 3.5 20.9 - - - -
160L TYR* 4.9 0.9 - - - +
59M GLU* 5.1 6.9 + - - -
61M GLY 5.5 2.9 + - - -
62M SER* 5.3 0.9 - - - -
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Residues in contact with MET 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L SER* 4.4 1.6 - - - -
135L PHE 3.3 11.9 - - - +
136L MET* 4.0 20.2 - - + -
149L TYR* 1.3 74.5 - - - +
151L ILE* 1.3 78.4 + - - +
152L ASP* 3.9 20.4 - - + +
156L VAL 3.3 3.5 - - - +
157L SER* 3.7 0.3 - - - -
158L TYR* 2.8 57.4 + - + -
160L TYR* 3.9 26.7 - - + +
163L CYS* 4.6 6.3 - - - -
165L ILE* 4.1 23.6 - - + -
169L ARG* 5.7 4.3 - - - +
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Residues in contact with ILE 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ALA* 4.0 34.5 - - + +
115L VAL* 5.2 0.4 - - + -
116L ALA* 4.0 9.6 - - + +
119L VAL* 4.1 16.8 - - + -
134L SER* 3.2 4.7 - - - -
135L PHE* 2.8 76.1 + - + +
137L LEU* 4.4 5.4 - - + -
150L MET* 1.3 84.0 - - - +
152L ASP* 1.3 75.1 + - - +
155L GLY* 4.4 6.3 - - - -
156L VAL 3.3 11.7 - - - +
157L SER* 3.9 13.0 - - - +
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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