Contacts of the strand formed by residues 44 - 49 (chain A) in PDB entry 5M4L
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 SER 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.2 4.3 - - - +
41A GLN* 2.8 27.0 + - - +
42A ALA 3.3 0.4 - - - -
43A GLY* 1.3 79.9 - - - +
45A ILE* 1.3 62.2 + - - +
87A ASP* 3.9 2.6 - - - +
88A VAL* 3.1 35.8 + - - +
89A ASP* 4.6 0.8 + - - -
142A SER* 3.7 1.7 + - - -
143A VAL* 3.1 31.7 - - - +
145A LEU* 4.0 20.4 - - - +
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Residues in contact with ILE 45 (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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43A GLY 4.1 1.6 - - - +
44A SER* 1.3 79.0 - - - +
46A VAL* 1.3 75.0 + - - +
47A VAL* 3.6 7.4 + - + +
85A VAL* 3.7 20.9 - - + -
86A ILE 3.4 11.7 - - - +
87A ASP* 4.0 16.2 - - - +
136A LEU* 4.1 13.9 - - + -
139A GLN* 3.3 32.3 - - + +
141A PRO* 3.7 28.0 - - + -
143A VAL 3.1 6.7 + - - -
144A LEU* 3.4 12.7 - - + -
145A LEU* 2.8 26.3 + - - -
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Residues in contact with VAL 46 (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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30A LEU* 4.6 9.0 - - + -
31A CYS* 6.0 1.1 - - - -
34A LEU* 3.8 29.4 - - + -
45A ILE* 1.3 70.9 - - - +
47A VAL* 1.3 59.7 + - - +
48A LEU* 4.2 17.7 - - + -
84A GLY 5.5 0.2 - - - +
85A VAL* 3.1 10.0 - - - +
86A ILE* 2.9 54.0 + - + +
88A VAL* 3.9 12.1 - - + +
145A LEU* 3.4 11.2 - - + -
176A LEU* 3.9 30.7 - - + -
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Residues in contact with VAL 47 (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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45A ILE* 3.8 14.1 - - + +
46A VAL* 1.3 77.3 - - - +
48A LEU* 1.3 70.9 + - - +
83A TYR* 4.9 2.0 - - + -
84A GLY 3.7 2.2 - - - -
85A VAL* 4.0 20.6 - - + -
132A ILE* 4.7 7.4 - - + -
136A LEU* 4.4 3.4 - - + -
144A LEU* 4.0 30.1 - - + -
145A LEU 2.9 15.6 + - - +
146A THR* 3.8 18.0 - - + -
147A LEU 4.5 0.9 + - - -
161A ALA* 3.8 25.3 - - + +
163A PHE* 4.6 16.6 - - + -
166A ILE* 5.7 0.7 - - + -
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Residues in contact with LEU 48 (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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30A LEU* 6.0 0.2 - - + -
46A VAL* 4.2 13.0 - - + -
47A VAL* 1.3 79.8 - - - +
49A GLN* 1.3 61.2 + - - +
68A GLU* 6.1 0.2 - - - +
70A PHE* 4.2 13.5 - - + +
71A PHE* 3.7 19.7 - - + +
74A ALA* 3.9 28.3 - - + -
75A PHE* 4.5 6.5 - - + -
83A TYR* 3.4 7.0 - - - +
84A GLY 2.9 36.8 + - - +
86A ILE* 5.4 1.1 - - + -
147A LEU* 4.1 24.9 - - + -
161A ALA* 4.1 4.0 - - - -
176A LEU* 4.0 22.2 - - + -
180A ILE* 4.4 12.3 - - + -
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Residues in contact with GLN 49 (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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48A LEU* 1.3 74.5 - - - +
50A GLY* 1.3 73.9 + - - +
52A GLU* 4.3 10.9 + - - +
68A GLU* 4.4 12.8 - - - +
71A PHE* 3.7 5.0 - - - -
82A CYS 4.3 0.7 - - - +
83A TYR* 3.1 41.0 + - + -
159A ARG* 3.4 47.0 + - - +
160A GLU 4.2 0.7 - - - +
161A ALA* 3.5 20.2 - - + +
162A SER* 3.1 25.9 + - - +
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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