Contacts of the strand formed by residues 44 - 50 (chain A) in PDB entry 4M92
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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43A TYR* 1.3 76.7 - - - +
45A MET* 1.3 63.0 + - - +
84A LYS 2.9 8.9 + - - -
85A LEU* 3.4 19.9 - - - -
86A PHE 3.2 22.3 + - - -
112A HIS* 2.7 34.4 + - - -
113A PHE 3.6 5.6 - - - -
115A PRO* 3.5 13.4 - - - +
145A THR* 3.9 9.2 - - - +
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Residues in contact with MET 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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15A LEU* 4.8 5.2 - - + -
25A PHE* 4.8 2.7 - - + -
27A MET* 4.8 2.2 - - + -
35A PHE 4.4 5.4 - - - +
36A ILE* 3.4 41.7 - - + -
41A ARG* 6.2 1.6 - - - +
43A TYR* 3.5 33.4 + - + -
44A SER* 1.3 72.7 - - - +
46A ILE* 1.3 64.3 + - - +
47A VAL* 3.8 9.1 + - + -
86A PHE* 3.5 38.4 - - + +
88A SER* 3.0 23.6 - - - -
111A MET 3.8 0.3 - - - +
112A HIS* 3.5 2.9 - - - -
113A PHE* 2.7 41.2 + - - +
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Residues in contact with ILE 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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45A MET* 1.3 75.1 - - - +
47A VAL* 1.3 68.6 + - - +
68A TYR* 3.1 23.8 + - + +
85A LEU* 4.1 17.9 - - + -
86A PHE 2.9 6.0 + - - +
87A PHE* 3.5 27.0 - - + -
88A SER 2.8 26.0 + - - -
110A PHE* 5.2 2.7 - - + -
111A MET 3.4 6.1 - - - +
112A HIS* 3.7 36.6 - - + -
140A TRP* 4.1 17.9 - - + -
141A ILE* 4.0 24.7 - - + -
145A THR* 4.9 1.1 - - + -
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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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32A PHE* 4.3 2.5 - - + -
36A ILE* 3.6 27.8 - - + -
45A MET* 3.8 2.9 - - + -
46A ILE* 1.3 82.7 - - - +
48A MET* 1.3 64.4 + - - +
49A PHE* 3.7 35.3 + - + -
68A TYR* 4.0 1.6 - - - -
88A SER* 3.4 10.8 - - - +
90A VAL* 4.0 19.7 - - + +
109A THR 3.6 1.6 - - - +
110A PHE* 3.4 4.6 - - - +
111A MET 2.9 31.4 + - - -
113A PHE* 3.7 24.0 - - + -
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Residues in contact with MET 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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47A VAL* 1.3 71.8 - - - +
49A PHE* 1.3 72.5 + - - +
50A THR* 3.7 21.2 + - + -
64A ALA* 4.2 2.7 - - - -
65A ASN* 3.4 42.6 - - + +
68A TYR* 3.6 37.3 + - + -
88A SER 3.0 7.3 + - - -
89A MET* 3.2 21.2 - - + +
90A VAL 2.9 24.4 + - - +
108A PRO* 4.8 2.9 - - + -
109A THR 3.5 4.0 - - - +
110A PHE* 3.4 36.8 - - + -
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Residues in contact with PHE 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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32A PHE* 4.1 5.4 - + - -
47A VAL* 3.7 30.3 - - + -
48A MET* 1.3 71.5 - - - +
50A THR* 1.3 58.8 + - - +
90A VAL* 3.4 11.9 - - + -
98A VAL* 3.9 14.8 - - + -
99A PHE* 3.7 26.5 - + + -
102A LEU* 3.4 29.2 - - + -
104A MET* 3.5 35.4 - - + -
106A SER 5.8 0.2 - - - +
107A ALA* 4.5 0.7 - - + -
108A PRO* 3.0 29.0 - - - +
109A THR* 2.8 28.2 + - - +
111A MET* 3.7 18.6 - - + -
113A PHE* 4.1 9.9 - + - -
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Residues in contact with THR 50 (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 MET* 4.1 24.4 - - + +
49A PHE* 1.3 76.2 - - - +
51A ALA* 1.3 67.7 + - - +
52A LEU* 3.3 35.6 - - + +
61A SER* 3.3 17.3 + - - -
89A MET* 4.3 7.9 - - - -
90A VAL 2.9 15.8 + - - +
91A ASP* 3.3 14.9 - - + +
92A TYR 2.8 24.6 + - - -
99A PHE* 3.6 4.6 - - - -
107A ALA* 3.9 9.2 - - - -
108A PRO* 4.6 0.8 - - - +
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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