Contacts of the strand formed by residues 35 - 44 (chain A) in PDB entry 1U3T
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 GLU 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PRO* 3.8 2.7 - - - -
32A LYS* 3.1 33.9 + - - +
33A ALA 3.3 9.6 - - - +
34A HIS* 1.3 83.5 - - - +
36A VAL* 1.3 68.6 + - - +
77A GLY 3.0 24.9 + - - -
80A VAL* 3.3 1.6 - - - +
123A LEU* 3.6 12.1 - - - +
125A ASP* 4.3 7.1 - - - +
129A ARG* 2.7 46.8 + - - -
151A VAL* 3.6 11.8 - - + +
152A VAL 3.3 10.5 - - - +
153A ASP* 4.0 15.0 - - - +
154A GLU 4.2 0.7 - - - +
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Residues in contact with VAL 36 (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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31A PRO* 4.3 0.7 - - - -
35A GLU* 1.3 82.9 - - - +
37A ARG* 1.3 65.6 + - - +
38A ILE* 3.9 13.5 + - + -
73A VAL* 3.7 29.2 - - + -
75A SER 3.7 3.6 - - - +
76A VAL* 4.4 2.7 - - + -
80A VAL* 4.0 16.2 - - + -
83A VAL* 3.7 26.5 - - + -
150A THR 3.6 0.9 - - - +
151A VAL* 3.2 5.1 - - - -
152A VAL* 2.8 39.8 + - + +
154A GLU* 4.5 5.8 - - - -
157A VAL* 4.2 19.3 - - + -
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Residues in contact with ARG 37 (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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2A THR 3.2 17.0 + - - -
4A GLY 4.1 8.3 - - - +
5A LYS 2.8 27.1 + - - -
7A ILE* 3.3 22.9 - - - +
28A VAL* 2.9 32.4 + - - -
29A ALA 3.6 6.1 + - - -
30A PRO* 3.7 9.1 - - - +
31A PRO* 3.8 8.3 - - + +
36A VAL* 1.3 71.9 - - - +
38A ILE* 1.3 61.9 + - - +
73A VAL* 3.8 4.2 - - - +
74A GLU* 2.7 54.1 + - + +
75A SER* 2.9 27.1 + - - +
149A TYR* 4.5 10.1 - - + -
150A THR 3.2 10.8 - - - +
151A VAL* 3.6 20.0 - - + +
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Residues in contact with ILE 38 (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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36A VAL* 4.0 14.8 - - + +
37A ARG* 1.3 78.6 - - - +
39A LYS* 1.3 72.4 + - - +
40A MET* 3.6 10.8 + - + +
71A GLY* 3.8 9.4 - - - -
72A ILE 3.5 18.6 - - - +
73A VAL* 5.0 0.4 - - - -
74A GLU* 4.8 0.2 - - - -
89A VAL* 3.7 15.9 - - + -
91A PRO* 4.1 22.0 - - + -
149A TYR* 3.3 9.8 - - - -
150A THR* 2.7 43.7 + - + +
152A VAL* 4.1 11.9 - - + -
157A VAL* 3.6 30.1 - - + -
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Residues in contact with LYS 39 (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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37A ARG 4.3 0.4 + - - -
38A ILE* 1.3 72.1 - - - +
40A MET* 1.3 68.0 + - - +
41A VAL* 3.6 6.4 + - + +
71A GLY* 3.1 2.9 - - - -
72A ILE* 2.8 45.5 + - + +
74A GLU* 4.5 5.3 - - + +
148A GLN* 3.4 8.1 - - + +
149A TYR* 3.4 40.3 + - + +
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Residues in contact with MET 40 (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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38A ILE* 3.6 15.2 + - + +
39A LYS* 1.3 79.5 - - - +
41A VAL* 1.3 61.9 + - - +
42A ALA 4.3 0.4 - - - +
69A ALA* 3.6 12.3 - - + -
70A ALA* 3.2 41.5 - - - +
71A GLY* 3.4 7.2 - - - +
91A PRO* 4.2 9.6 - - + -
145A THR* 3.6 33.0 - - - +
147A SER 3.2 19.3 - - - +
148A GLN* 2.9 10.5 + - - +
150A THR* 4.5 14.6 - - - -
374A PHE* 3.3 41.3 - - + +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS* 4.0 8.7 - - + +
40A MET* 1.3 77.5 - - - +
42A ALA* 1.3 64.2 + - + +
70A ALA 2.9 12.0 + - - +
71A GLY* 3.9 9.6 - - - -
72A ILE* 4.4 12.1 - - + +
166A LEU* 3.7 37.5 - - + -
167A GLU* 5.4 1.3 - - + +
373A MET* 3.7 10.7 - - - +
374A PHE* 3.1 28.6 + - - +
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Residues in contact with ALA 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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40A MET* 4.3 1.2 - - - +
41A VAL* 1.3 81.2 - - + +
43A VAL* 1.3 60.5 + - - +
69A ALA* 3.1 6.6 - - - +
70A ALA 3.0 29.0 + - - +
166A LEU 3.5 26.2 - - - +
167A GLU* 3.8 15.3 - - - -
170A CYS* 4.2 3.6 - - - -
371A ILE* 3.9 13.2 - - + -
372A LEU 3.4 7.0 - - - +
373A MET* 4.2 4.9 - - - -
374A PHE* 4.3 1.6 - - - -
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Residues in contact with VAL 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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42A ALA* 1.3 77.7 - - - +
44A GLY* 1.3 69.2 + - - +
67A HIS 4.6 0.7 - - - +
68A GLU 3.2 17.3 - - - +
69A ALA* 3.8 3.8 - - + -
145A THR* 3.2 27.8 - - - +
146A PHE* 3.8 23.6 - - + -
170A CYS* 4.8 0.9 - - - -
371A ILE* 4.2 3.5 - - - +
372A LEU* 2.8 51.3 + - + +
374A PHE* 3.5 28.5 - - + -
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Residues in contact with GLY 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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43A VAL* 1.3 87.1 - - - +
45A ILE* 1.3 63.6 + - - +
46A CYS 3.8 2.1 + - - -
49A ASP* 4.1 6.4 - - - +
68A GLU* 2.7 37.3 + - - +
146A PHE* 4.1 1.7 - - - -
170A CYS* 4.5 1.8 - - - -
369A ARG* 5.1 0.4 - - - -
370A THR 3.6 7.6 - - - -
371A ILE* 3.8 15.2 - - - +
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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