Contacts of the strand formed by residues 138 - 145 (chain A) in PDB entry 1UMK
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 THR 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PRO* 4.1 24.8 - - + +
44A LEU 3.2 9.4 - - - +
45A ARG* 3.5 29.4 - - + +
129A TYR* 4.5 10.9 + - - -
133A MET* 3.7 7.5 - - - +
136A GLY 4.1 2.2 - - - +
137A ASP* 1.3 76.7 - - - +
139A ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 139 (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 TYR 3.5 1.0 - - - +
43A PRO* 4.1 1.3 - - - -
44A LEU 3.0 24.0 + - - -
61A PHE* 3.6 32.1 - - + -
80A LEU* 4.0 11.9 - - + -
81A SER 3.7 13.7 - - - +
82A ALA* 4.7 0.4 - - + -
126A MET* 3.8 21.8 - - - -
129A TYR* 3.8 31.2 - - + -
130A LEU* 4.1 15.5 - - + -
133A MET* 3.9 6.5 - - + -
138A THR* 1.3 74.7 - - - +
140A GLU* 1.3 70.4 + - - +
141A PHE* 3.6 17.1 - - + -
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Residues in contact with GLU 140 (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 LYS* 3.6 37.7 - - + +
42A TYR 3.4 2.7 - - - +
43A PRO* 4.1 23.2 - - + +
79A TYR 3.5 0.5 - - - +
80A LEU* 3.3 8.7 - - - +
81A SER* 3.1 50.3 + - - +
82A ALA* 5.2 2.9 - - - -
83A ARG* 5.4 5.5 + - - -
88A LEU* 6.1 0.7 - - - +
139A ILE* 1.3 77.9 - - - +
141A PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 141 (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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35A LEU* 4.6 12.3 - - + -
41A LYS* 3.5 4.3 - - - -
42A TYR* 2.8 41.6 + - + +
44A LEU* 3.6 31.4 - - + -
61A PHE* 3.8 27.1 - + - -
70A LEU* 4.9 5.8 - - + -
78A ILE* 3.7 37.2 - - + -
79A TYR 3.4 4.0 - - - -
80A LEU* 3.5 18.6 - - + -
105A VAL* 4.0 24.0 - - + -
107A LEU* 4.2 9.6 - - + -
139A ILE* 3.6 23.1 - - + -
140A GLU* 1.3 72.6 - - - +
142A ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 142 (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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35A LEU* 4.5 3.6 - - - -
38A PRO 2.7 20.0 + - - +
39A ASP* 3.1 34.6 + - - +
40A ILE 3.7 15.3 - - - +
41A LYS* 4.4 33.8 - - + +
78A ILE* 3.4 7.2 - - - -
79A TYR* 2.8 50.0 + - + +
81A SER* 5.9 2.0 - - - +
90A VAL* 6.5 0.9 - - - -
141A PHE* 1.3 75.6 - - - +
143A GLY* 1.3 60.8 + - - +
145A SER* 4.7 2.4 + - - +
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Residues in contact with GLY 143 (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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35A LEU* 3.8 23.6 - - - +
37A SER 3.9 3.8 - - - +
38A PRO* 3.6 22.5 - - - +
40A ILE 5.1 0.8 + - - -
77A HIS 4.6 0.7 - - - -
78A ILE* 4.8 0.2 - - - -
142A ARG* 1.3 81.6 - - - +
144A PRO* 1.3 77.8 - - - +
145A SER* 4.0 5.8 - - - -
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Residues in contact with PRO 144 (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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35A LEU* 4.0 10.9 - - + +
38A PRO* 5.0 11.8 - - + +
71A GLY 4.2 11.9 - - - +
72A LEU* 3.6 23.1 - - + -
73A PRO* 3.7 15.5 - - + -
76A GLN* 3.5 27.2 + - - +
77A HIS 3.6 5.2 - - - +
143A GLY* 1.3 83.7 - - - +
145A SER* 1.3 65.8 + - - +
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Residues in contact with SER 145 (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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76A GLN* 3.2 10.7 - - - +
77A HIS* 2.9 52.5 + - - -
79A TYR* 3.8 24.7 - - - -
142A ARG* 4.7 0.5 + - - +
143A GLY* 4.0 7.1 - - - -
144A PRO* 1.3 79.1 + - - +
146A GLY* 1.3 59.8 + - - +
162A LYS* 5.6 5.1 + - - -
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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