Contacts of the strand formed by residues 128 - 134 (chain A) in PDB entry 1UMZ
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 HIS 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLN* 3.2 5.5 - - - -
60A MET 2.9 30.2 + - - -
121A PHE* 3.3 53.1 - + + +
122A ASP 4.6 2.4 + - - -
123A PRO* 4.9 1.1 - - + -
126A GLU* 3.2 40.1 - - - +
127A PHE* 1.3 78.0 + - - +
129A TYR* 1.3 63.6 + - - +
130A TYR* 3.5 25.3 - - + +
144A ASP* 2.8 28.8 + - - +
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Residues in contact with TYR 129 (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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6A PRO* 4.1 22.2 + - + -
8A ASP* 3.0 23.6 + - - -
57A SER* 3.4 20.6 - - - +
58A MET 3.5 3.6 - - - -
59A GLN* 3.3 39.5 + - + -
128A HIS* 1.3 73.6 - - - +
130A TYR* 1.3 63.0 + - - +
131A SER* 4.5 4.7 - - - +
143A VAL* 3.4 5.5 - - - +
144A ASP* 2.8 52.6 + - - +
201A SER* 3.8 17.3 - - - -
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Residues in contact with TYR 130 (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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57A SER* 3.4 0.3 - - - -
58A MET 2.8 33.2 + - - +
60A MET* 3.8 34.7 + - + -
62A LEU* 4.5 2.0 - - + +
74A PHE* 3.4 19.7 - - + -
88A PHE* 4.2 17.5 - + + -
90A PHE* 3.5 34.2 - + + -
101A LEU* 4.3 3.4 - - + -
119A LEU* 3.9 2.3 - - + +
121A PHE* 3.5 25.4 - + - -
123A PRO* 3.9 13.7 - - - +
128A HIS* 3.5 28.4 - - + +
129A TYR* 1.3 74.8 - - - +
131A SER* 1.3 60.5 + - - +
142A LEU 3.4 3.1 - - - -
143A VAL* 3.8 32.8 - - + -
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Residues in contact with SER 131 (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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6A PRO* 4.9 2.8 - - - +
55A HIS* 4.3 13.1 + - - -
56A PHE 3.2 9.6 - - - -
57A SER* 2.8 25.1 + - - -
74A PHE* 4.7 0.4 - - - -
88A PHE* 3.4 9.5 - - - -
129A TYR* 4.5 5.9 - - - +
130A TYR* 1.3 74.3 + - - +
132A VAL* 1.3 64.6 + - - +
140A VAL 4.4 0.2 - - - -
141A PHE* 3.6 0.7 - - - -
142A LEU* 2.9 51.2 + - - +
144A ASP 5.1 2.8 + - - -
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Residues in contact with VAL 132 (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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54A GLY 3.8 1.0 - - - +
55A HIS* 3.5 7.9 - - - -
56A PHE* 2.9 38.8 + - + +
74A PHE* 4.9 4.5 - - + -
75A TYR* 6.5 0.2 - - - -
76A LEU* 4.2 21.3 - - + -
86A ILE* 4.0 34.8 - - + +
88A PHE* 3.7 22.9 - - + -
131A SER* 1.3 77.8 - - - +
133A LEU* 1.3 71.1 - - - +
134A TRP* 4.2 11.0 - - + -
139A ILE* 4.1 11.0 - - + -
140A VAL 3.3 4.7 - - - +
141A PHE* 4.9 2.0 - - + -
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Residues in contact with LEU 133 (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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54A GLY 3.6 12.6 - - - +
55A HIS* 4.1 12.6 - - + -
131A SER 4.3 0.2 - - - -
132A VAL* 1.3 73.7 - - - +
134A TRP* 1.3 60.1 + - - +
135A ASN* 4.1 13.5 - - - +
138A MET* 3.7 7.9 - - + +
139A ILE* 3.2 4.7 - - - +
140A VAL* 2.8 56.1 + - + +
142A LEU* 4.5 7.9 - - + +
223A TRP* 4.0 26.2 - - + -
224A TRP* 4.1 14.4 - - + -
229A PHE* 3.8 31.6 - - + -
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Residues in contact with TRP 134 (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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51A TYR 3.3 27.8 - - - -
52A LEU* 3.8 22.2 - - + -
53A PHE* 3.2 35.6 - + - +
54A GLY 2.9 40.1 + - - +
56A PHE* 4.1 6.5 - + + -
76A LEU* 4.0 17.5 - - + -
86A ILE* 4.2 1.6 - - + -
132A VAL* 4.2 14.1 - - + -
133A LEU* 1.3 73.7 - - - +
135A ASN* 1.3 67.9 + - - +
138A MET 3.7 2.2 - - - -
139A ILE* 3.6 22.9 - - + -
161A PHE* 4.4 0.2 - + - -
162A PRO* 2.9 33.4 + - + +
165A GLN 4.2 2.2 - - - -
167A MET* 3.3 46.9 - - + -
224A TRP* 4.4 1.4 - - - -
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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