Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 1W31
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 LEU 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.4 19.7 - - + -
37A THR 4.1 4.9 - - - +
38A LYS* 3.2 19.8 + - - +
39A ASN 4.6 3.5 - - - +
40A MET* 1.3 83.0 - - - +
42A ILE* 1.3 63.6 + - - +
43A PHE 4.2 0.9 - - - -
83A LEU* 4.3 8.3 - - + +
84A ARG* 4.9 1.4 + - - +
85A SER* 4.1 16.5 + - - +
315A HIS* 5.1 1.3 - - + -
326A ILE* 3.5 11.2 - - + +
328A THR* 4.2 19.3 - - + -
331A ALA* 4.2 22.2 - - + +
334A PHE* 3.6 35.0 - - + -
335A LEU* 4.3 11.9 - - + -
338A LEU* 4.1 12.1 - - + -
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Residues in contact with ILE 42 (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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39A ASN 6.1 0.2 - - - +
40A MET 4.3 2.7 - - - +
41A LEU* 1.3 79.5 - - - +
43A PHE* 1.3 59.4 + - - +
44A PRO* 3.4 4.3 - - - +
85A SER* 3.7 26.7 - - - +
86A VAL 4.0 0.9 - - - -
87A ILE* 3.9 22.0 - - + +
129A ILE* 3.9 22.9 - - + -
205A LEU* 5.2 2.7 - - + -
285A CYS* 4.1 14.6 - - - -
325A LEU* 4.4 23.6 - - + -
326A ILE 2.8 9.5 + - - +
327A ILE* 3.3 32.1 - - + +
328A THR 3.2 23.8 + - - +
331A ALA* 4.9 1.6 - - - -
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Residues in contact with PHE 43 (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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41A LEU 4.2 0.6 - - - -
42A ILE* 1.3 70.7 - - - +
44A PRO* 1.3 92.0 - - + +
45A LEU* 4.2 8.1 - - + -
63A ILE* 4.2 16.2 - - + -
74A TYR* 3.4 32.8 - + - -
75A LEU* 5.4 0.2 - - + -
78A LEU* 3.6 30.5 - - + -
83A LEU* 4.0 21.4 - - + +
85A SER 3.3 7.4 + - - +
86A VAL* 3.2 10.1 - - + +
87A ILE* 3.1 20.5 + - - -
328A THR 3.6 9.4 - - - -
329A TYR* 3.8 17.3 - + - -
331A ALA* 3.8 10.5 - - + +
332A PRO* 3.6 29.2 - - + -
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Residues in contact with PRO 44 (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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42A ILE 3.4 3.8 - - - +
43A PHE* 1.3 103.9 - - + +
45A LEU* 1.3 70.8 + - - +
46A PHE* 4.4 8.0 + - + -
63A ILE* 5.6 1.9 - - - +
87A ILE* 3.4 14.6 - - + -
89A PHE* 4.2 11.9 - - + -
287A TYR* 4.2 1.3 - - - +
327A ILE* 3.7 24.5 - - + -
328A THR 3.3 21.1 - - - +
329A TYR* 3.5 34.8 - - + -
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Residues in contact with LEU 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 PHE* 4.2 15.9 - - + +
44A PRO* 1.3 84.3 - - - +
46A PHE* 1.3 60.9 + - - +
47A ILE* 3.7 7.1 + - + +
66A ILE* 5.6 3.6 - - + -
71A LEU* 4.1 17.5 - - + -
74A TYR* 3.9 28.9 - - + -
75A LEU* 3.8 27.4 - - + -
86A VAL* 4.2 12.3 - - + -
87A ILE 2.9 9.1 + - - -
88A LEU* 3.4 29.5 - - + -
89A PHE* 2.7 35.2 + - - +
119A ILE* 4.4 4.3 - - + -
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Residues in contact with PHE 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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44A PRO* 4.4 7.2 - - + -
45A LEU* 1.3 72.7 - - - +
47A ILE* 1.3 63.8 + - - +
57A ILE* 4.6 0.7 - - + -
60A LEU* 3.8 15.0 - - + -
63A ILE* 3.9 17.0 - - + -
64A ASN 4.0 13.0 + - - +
65A ARG* 3.5 7.4 - - - -
66A ILE* 3.0 29.0 + - - +
89A PHE* 3.4 27.4 - + + -
91A VAL* 4.1 13.0 - - + -
219A PHE* 3.3 34.3 - + - -
222A ALA* 4.1 26.0 - - + +
223A ALA* 4.6 2.2 - - + -
329A TYR* 3.4 42.2 - + - -
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Residues in contact with ILE 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 LEU* 4.3 14.8 - - + +
46A PHE* 1.3 75.4 - - - +
48A SER* 1.3 63.0 + - - +
66A ILE* 3.2 9.0 - - + +
68A VAL* 4.5 16.4 - - + +
71A LEU* 3.8 38.4 - - + -
88A LEU* 4.4 24.7 - - + -
89A PHE 2.9 12.6 + - - +
91A VAL* 2.7 33.2 + - - -
111A PRO* 3.3 41.2 - - + +
112A VAL* 4.8 1.1 - - - +
115A GLY* 5.0 2.5 - - - -
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Residues in contact with SER 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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46A PHE 3.7 0.4 + - - -
47A ILE* 1.3 81.4 - - - +
49A ASP* 1.3 60.6 + - - +
50A ASN 3.0 10.5 + - - -
51A PRO 4.7 0.2 - - - -
53A ASP* 2.7 34.9 + - - -
65A ARG* 3.4 18.8 - - - -
66A ILE 2.7 15.9 + - - +
67A GLY* 4.1 6.1 - - - -
68A VAL* 4.8 3.3 + - - +
91A VAL* 3.4 6.1 - - - -
93A LEU* 2.9 18.7 - - - +
111A PRO* 3.8 9.1 - - - +
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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