Contacts of the strand formed by residues 51 - 61 (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 TYR 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN* 4.9 7.1 + - - -
47A SER* 4.2 0.4 - - - -
49A GLY* 3.4 32.0 + - - -
50A SER* 1.3 78.8 - - - +
52A LEU* 1.3 59.9 + - - +
53A PHE 3.9 2.9 - - - +
56A PHE* 3.8 22.9 - + + -
134A TRP* 3.3 9.1 - - + -
166A PRO* 3.3 4.2 - - - +
167A MET 2.8 32.4 + - - +
169A ILE* 3.7 24.9 - - + -
204A ILE* 3.5 34.5 - - + +
206A GLY* 3.7 28.7 - - - -
207A CYS 3.3 4.0 - - - +
208A GLU* 3.5 29.0 - - + +
209A ALA* 4.3 0.7 - - - +
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Residues in contact with LEU 52 (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* 1.3 72.7 - - - +
53A PHE* 1.3 84.7 + - + +
134A TRP* 3.8 14.8 - - + -
163A PHE 3.7 19.1 - - - +
164A ASN* 4.0 17.7 - - + +
165A GLN 3.7 31.9 - - - +
166A PRO* 4.5 3.6 - - + -
207A CYS* 2.9 27.6 + - + +
209A ALA* 4.2 13.4 - - + +
214A LYS 4.0 23.8 - - - +
215A PHE* 4.7 5.2 - - - -
216A CYS* 5.4 3.6 - - + +
219A GLN* 4.3 3.1 + - + +
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Residues in contact with PHE 53 (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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52A LEU* 1.3 87.4 + - + +
54A GLY* 1.3 57.9 + - - +
56A PHE* 3.9 9.5 - - - -
134A TRP* 3.2 51.0 - + - +
135A ASN* 3.5 28.5 - - - -
136A MET* 3.9 18.6 - - + -
161A PHE* 4.6 0.4 - + - -
162A PRO 3.9 7.2 - - - -
163A PHE* 3.6 28.7 - + - -
206A GLY* 3.5 2.1 - - - -
207A CYS 3.0 25.1 + - - -
219A GLN* 3.2 38.4 - - - +
224A TRP* 3.7 17.9 - + - +
225A ASP* 5.2 1.1 - - - -
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Residues in contact with GLY 54 (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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53A PHE* 1.3 74.6 - - - +
55A HIS* 1.3 59.1 + - - -
56A PHE* 3.3 17.6 - - - -
133A LEU* 3.6 6.0 - - - +
134A TRP 2.9 35.0 + - - +
205A ASP 3.3 12.1 - - - -
206A GLY* 3.8 1.8 - - - -
224A TRP* 3.8 13.8 - - - -
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Residues in contact with HIS 55 (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 30.5 - - + +
54A GLY* 1.3 73.2 - - - +
56A PHE* 1.3 65.7 + - - +
57A SER* 4.9 0.4 - - - -
131A SER* 4.3 16.0 + - - -
132A VAL 3.5 17.0 - - - -
133A LEU* 4.1 12.1 - - + -
142A LEU* 5.6 3.9 - - + +
203A HIS* 3.6 19.8 - + - -
205A ASP* 2.8 37.6 + - + +
223A TRP* 3.7 38.1 - + + -
224A TRP* 4.5 0.2 - - - -
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Residues in contact with PHE 56 (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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15A TYR* 5.9 0.4 - - - +
51A TYR* 3.8 25.1 - + + -
53A PHE 3.9 3.1 - - - -
54A GLY* 3.3 39.3 - - - -
55A HIS* 1.3 76.2 - - - +
57A SER* 1.3 61.2 + - - +
74A PHE* 4.3 10.6 - - + -
76A LEU* 3.8 31.2 - - + -
130A TYR 4.2 0.2 - - - +
131A SER* 3.2 3.6 - - - -
132A VAL* 2.9 48.3 + - + +
134A TRP* 4.1 9.0 - + + -
169A ILE* 3.6 34.3 - - + -
203A HIS 3.6 5.2 - - - +
204A ILE* 3.8 23.6 - - + -
206A GLY* 4.5 2.5 - - - -
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Residues in contact with SER 57 (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* 3.9 12.4 - - - +
15A TYR* 5.3 0.9 + - - -
55A HIS* 4.9 1.8 - - - -
56A PHE* 1.3 73.3 - - - +
58A MET* 1.3 64.2 + - - +
74A PHE* 4.3 4.6 - - - -
129A TYR* 3.4 22.2 - - - -
130A TYR 3.4 5.8 + - - -
131A SER* 2.8 23.8 + - - -
201A SER* 4.3 1.7 + - - -
202A PHE* 3.9 2.3 + - - -
203A HIS* 3.0 53.7 + - - +
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Residues in contact with MET 58 (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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15A TYR* 3.7 31.4 - - + +
45A PHE* 4.0 20.6 - - + -
57A SER* 1.3 78.4 + - - +
59A GLN* 1.3 64.8 + - - +
60A MET* 3.6 13.9 + - + -
74A PHE* 3.9 33.4 - - + -
128A HIS 3.6 0.5 - - - +
129A TYR* 3.5 1.3 - - - -
130A TYR* 2.8 33.2 + - - +
169A ILE* 5.2 0.2 - - + -
199A TYR* 3.5 26.9 - - + -
200A ARG 3.7 9.2 - - - +
202A PHE* 3.5 30.3 - - + +
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Residues in contact with GLN 59 (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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8A ASP* 3.8 15.4 + - - -
58A MET* 1.3 72.3 - - - +
60A MET* 1.3 60.7 + - - +
127A PHE* 3.5 27.7 - - + +
128A HIS 3.2 8.3 - - - +
129A TYR* 3.3 52.6 + - + -
199A TYR* 3.2 5.4 - - - -
200A ARG* 2.8 68.7 + - + +
201A SER* 3.9 2.6 - - - -
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Residues in contact with MET 60 (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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58A MET* 3.6 21.3 + - + -
59A GLN* 1.3 80.8 - - - +
61A LYS* 1.3 61.0 + - - +
62A LEU* 4.1 9.7 - - + +
72A THR* 3.7 30.1 - - + -
73A ALA 4.9 1.1 - - - +
74A PHE* 3.9 27.1 - - + -
90A PHE* 3.7 25.6 - - + -
123A PRO 4.4 1.0 - - - +
126A GLU 3.8 1.9 - - - +
127A PHE* 3.5 4.8 - - - -
128A HIS* 2.9 27.6 + - - +
130A TYR* 3.8 26.1 + - + -
171A SER* 4.7 0.2 - - - +
198A SER 3.2 6.3 - - - +
199A TYR* 3.7 21.3 - - + +
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Residues in contact with LYS 61 (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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32A GLU* 4.9 3.4 + - - -
60A MET* 1.3 73.8 - - - +
62A LEU* 1.3 67.4 + - - +
123A PRO 3.6 3.6 - - - -
124A THR 3.5 25.6 - - - +
125A LYS 3.9 9.7 + - - +
126A GLU* 3.8 25.1 - - - +
127A PHE* 3.6 38.4 - - + -
197A ALA* 3.8 1.2 - - - +
198A SER* 2.9 43.8 + - - +
200A ARG* 5.6 0.6 - - - +
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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