Contacts of the strand formed by residues 133 - 144 (chain B) in PDB entry 5UHE
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 LYS 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ASP* 5.0 5.8 - - - -
66B VAL* 4.4 3.5 - - - +
67B PRO 3.5 19.1 + - - +
100B GLN* 3.6 33.8 + - + +
128B LEU* 4.5 1.7 - - - +
131B LYS 3.9 4.1 + - - +
132B GLY* 1.3 71.5 - - - -
134B LEU* 1.3 74.6 + - - +
135B GLU* 3.0 31.5 + - + +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ILE* 4.8 6.1 - - + -
66B VAL* 3.6 32.1 - - + -
69B VAL* 3.8 11.4 - - + -
76B ILE* 6.1 3.8 - - + -
97B LEU 3.8 1.5 - - - +
98B ARG* 3.4 3.8 - - - -
99B LYS* 3.1 40.5 + - + +
105B VAL* 4.4 15.0 - - + -
125B ILE* 6.3 0.7 - - + -
126B ALA* 4.5 13.2 - - + -
128B LEU* 3.8 26.9 - - + -
133B LYS* 1.3 78.8 - - - +
135B GLU* 1.3 64.2 + - - +
136B VAL* 4.3 17.3 - - + -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG 3.8 2.4 - - - +
56B ILE* 3.9 1.6 - - - +
57B ASP* 3.0 53.8 + - + +
97B LEU 3.8 3.1 - - - -
98B ARG* 3.9 29.9 - - + +
133B LYS* 3.0 34.2 + - + +
134B LEU* 1.3 79.7 - - - +
136B VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 4.5 9.2 - - + -
55B ARG 3.4 15.0 - - - +
56B ILE* 4.9 12.3 - - + -
76B ILE* 6.4 1.8 - - + -
80B LEU* 5.1 4.5 - - + -
95B MET 4.1 0.2 - - - +
96B TYR* 3.6 8.3 - - - -
97B LEU* 3.0 45.8 + - + +
98B ARG* 5.0 1.0 - - - +
134B LEU* 4.5 18.8 - - + -
135B GLU* 1.3 84.1 - - - +
137B GLU* 1.3 64.0 + - - +
138B LEU* 3.6 27.6 + - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 3.4 7.1 - - - +
55B ARG* 3.1 75.9 + - + -
94B THR* 3.7 24.8 + - + +
95B MET 3.9 2.5 - - - -
96B TYR* 3.7 27.0 + - + -
136B VAL* 1.3 74.6 - - - +
138B LEU* 1.3 64.6 + - - +
139B VAL* 4.5 10.9 - - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 5.0 9.4 - - + -
53B SER 4.1 1.3 - - - +
54B ILE* 3.6 25.8 - - + -
80B LEU* 4.1 17.3 - - + -
83B LEU* 4.8 7.9 - - + -
94B THR* 3.2 12.3 - - - +
95B MET* 2.8 69.4 + - + +
97B LEU* 5.1 9.0 - - + -
110B ILE* 4.6 18.2 - - + -
136B VAL* 3.6 24.7 - - + +
137B GLU* 1.3 74.5 - - - +
139B VAL* 1.3 63.6 + - - +
140B VAL* 4.0 3.4 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.7 3.9 - - - +
52B THR* 2.9 36.3 + - + -
53B SER* 2.9 40.1 + - - +
54B ILE* 5.4 1.1 - - - -
55B ARG* 6.1 2.9 - - + -
92B PRO* 4.7 14.6 - - + -
93B VAL 3.8 8.7 - - - +
94B THR* 4.4 9.0 - - - +
137B GLU* 4.5 14.6 - - + +
138B LEU* 1.3 76.2 - - - +
140B VAL* 1.3 63.2 + - - +
141B GLU* 4.7 4.5 - - + +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 4.2 15.3 - - + -
50B ALA 3.6 12.8 - - - +
51B VAL* 4.9 11.2 - - + -
85B VAL* 4.3 13.2 - - + -
87B SER* 4.2 15.8 + - - -
91B GLU 4.7 0.3 - - - +
92B PRO* 3.3 5.9 - - - +
93B VAL* 3.1 43.0 + - + +
95B MET* 3.8 38.4 - - + -
138B LEU* 4.0 1.5 - - + -
139B VAL* 1.3 73.8 - - - +
141B GLU* 1.3 72.8 + - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.3 38.0 - - + +
186A ARG* 4.9 5.6 + - - -
49B ALA* 3.4 24.8 - - - +
50B ALA 3.2 12.1 + - - -
52B THR* 3.3 35.7 + - - +
87B SER* 5.7 0.2 - - - -
90B ASP 4.9 2.5 - - - +
92B PRO* 3.8 28.6 - - + +
139B VAL* 3.9 6.3 + - + +
140B VAL* 1.3 79.0 - - - +
142B ARG* 1.3 65.4 + - - +
152B ASN* 5.2 0.2 - - - +
168B TYR* 3.8 9.9 + - + -
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.5 23.7 - - - +
5A GLN* 5.6 4.0 - - - +
47B PRO* 4.4 25.6 + - + +
48B GLY* 3.4 27.3 + - - +
49B ALA* 4.2 6.3 - - + -
86B SER* 5.5 1.6 - - - +
87B SER* 2.8 38.6 + - - +
88B GLU 4.9 2.8 + - - -
89B GLU 3.5 27.6 - - - +
90B ASP* 3.6 34.9 + - - +
141B GLU* 1.3 79.3 - - - +
143B GLY* 1.3 58.8 + - - +
168B TYR* 3.7 4.6 - - - -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.9 10.3 - - - -
47B PRO* 3.2 7.4 - - - +
48B GLY 3.2 25.5 + - - -
142B ARG* 1.3 76.3 - - - +
144B ARG* 1.3 64.8 + - - -
168B TYR* 3.2 27.5 - - - +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE 5.7 2.0 - - - +
4A SER 4.9 5.9 + - - -
5A GLN* 3.1 39.0 - - - +
27A GLU* 3.6 28.9 + - - +
44B SER 3.1 17.5 - - - +
45B SER* 3.8 14.7 + - - +
46B ILE 3.8 4.7 - - - +
47B PRO* 3.2 42.8 - - + +
143B GLY* 1.3 80.4 - - - +
145B GLY* 1.3 64.8 + - - +
146B TYR 3.3 3.3 + - - +
147B VAL* 4.6 6.1 - - - +
168B TYR* 3.6 11.1 - - - -
624D ARG* 5.2 2.8 + - - -
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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