Contacts of the strand formed by residues 51 - 61 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN* 4.7 8.0 + - - -
47B SER* 4.3 2.2 - - - -
49B GLY* 3.5 31.4 + - - -
50B SER* 1.3 76.5 - - - +
52B LEU* 1.3 60.7 + - - +
53B PHE 4.0 2.5 - - - +
56B PHE* 4.0 21.5 - + + -
76B LEU* 5.8 0.2 - - + -
134B TRP* 3.5 7.6 - - + -
166B PRO* 3.3 5.2 - - - +
167B MET 2.8 31.9 + - - +
169B ILE* 3.5 28.9 - - + -
204B ILE* 3.4 31.3 - - + +
206B GLY* 3.7 26.7 - - - -
207B CYS 3.3 5.4 - - - +
208B GLU* 3.7 35.0 + - + -
209B ALA* 4.3 0.4 - - - +
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Residues in contact with LEU 52 (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 TYR* 1.3 72.3 - - - +
53B PHE* 1.3 84.9 - - + +
134B TRP* 3.8 18.2 - - + -
163B PHE 3.7 24.0 - - - +
164B ASN* 4.4 1.8 - - - -
165B GLN 3.7 31.9 - - - +
166B PRO* 3.8 7.0 - - + -
207B CYS* 2.9 25.9 + - - +
209B ALA* 4.3 12.0 - - + +
214B LYS* 3.9 4.3 - - - -
215B PHE* 3.4 44.2 - - - +
216B CYS* 3.6 6.7 - - + +
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Residues in contact with PHE 53 (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 TYR* 4.3 0.2 - - - +
52B LEU* 1.3 92.8 + - + +
54B GLY* 1.3 58.6 + - - +
56B PHE* 3.8 9.6 - - - -
134B TRP* 3.3 51.1 - + - +
135B ASN* 3.6 29.4 - - - -
136B MET* 3.8 26.2 - - + -
162B PRO 3.9 7.2 - - - -
163B PHE* 3.6 20.6 - - + -
206B GLY* 3.4 2.8 - - - -
207B CYS* 3.0 24.9 + - + -
215B PHE* 6.1 0.2 - - - -
216B CYS* 4.1 9.0 - - + -
219B GLN* 3.3 31.2 - - - -
224B TRP* 3.7 18.4 - + - +
225B ASP* 5.6 0.2 - - - -
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Residues in contact with GLY 54 (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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53B PHE* 1.3 76.2 - - - +
55B HIS* 1.3 60.5 + - - -
56B PHE* 3.3 15.1 - - - -
133B LEU* 3.5 4.5 - - - +
134B TRP 2.8 37.3 + - - +
205B ASP 3.4 11.0 - - - -
224B TRP* 3.7 18.7 - - - -
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Residues in contact with HIS 55 (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 GLY* 1.3 72.9 - - - +
56B PHE* 1.3 63.8 + - - +
57B SER* 4.9 5.2 - - - -
131B SER* 4.2 17.8 + - - -
132B VAL 3.4 16.8 - - - -
133B LEU* 4.0 13.5 - - + -
142B LEU* 5.5 3.4 - - + +
203B HIS* 3.8 27.1 + + - -
205B ASP* 2.8 37.9 + - + +
223B TRP* 3.7 37.7 - + + -
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Residues in contact with PHE 56 (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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15B TYR* 6.0 0.4 - - - +
51B TYR* 4.0 21.5 - + + -
53B PHE 3.8 19.3 - - - -
54B GLY* 3.3 28.9 - - - -
55B HIS* 1.3 77.2 - - - +
57B SER* 1.3 61.1 + - - +
74B PHE* 4.2 11.0 - - + -
76B LEU* 3.9 32.8 - - + -
130B TYR 4.1 0.2 - - - +
131B SER* 3.1 4.6 - - - -
132B VAL* 2.9 45.4 + - + +
134B TRP* 4.1 10.3 - + + -
169B ILE* 3.8 32.3 - - + -
203B HIS 3.7 5.2 - - - +
204B ILE* 4.0 16.4 - - + -
206B GLY* 4.4 4.5 - - - -
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Residues in contact with SER 57 (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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15B TYR* 5.2 0.9 + - - -
55B HIS* 4.8 6.7 - - - -
56B PHE* 1.3 75.2 - - - +
58B MET* 1.3 64.2 + - - +
74B PHE* 4.2 4.7 - - - -
129B TYR* 3.4 25.8 - - - -
130B TYR 3.4 10.6 + - - -
131B SER* 3.5 14.0 - - - -
201B SER* 4.9 1.1 - - - -
202B PHE* 4.0 1.6 - - - -
203B HIS* 3.0 55.3 + - - +
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Residues in contact with MET 58 (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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15B TYR* 3.9 15.7 - - + +
45B PHE* 3.8 17.3 - - + -
57B SER* 1.3 76.7 + - - +
59B GLN* 1.3 63.7 + - - +
60B MET* 3.6 13.8 + - + -
74B PHE* 3.9 30.0 - - + -
128B HIS 3.6 0.7 - - - +
129B TYR* 3.6 1.5 - - - -
130B TYR* 2.8 33.8 + - - +
171B SER* 3.6 22.7 - - - +
199B TYR* 3.6 20.9 - - + -
200B ARG 3.7 8.1 - - - +
201B SER* 4.8 0.4 - - - -
202B PHE* 3.5 34.5 - - - +
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Residues in contact with GLN 59 (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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58B MET* 1.3 72.5 - - - +
60B MET* 1.3 60.6 + - - +
127B PHE* 3.4 28.1 - - + +
128B HIS 3.2 11.2 - - - +
129B TYR* 3.4 48.5 + - + -
199B TYR* 3.3 4.2 - - - -
200B ARG* 2.8 69.5 + - + +
201B SER* 4.0 9.4 - - - +
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Residues in contact with MET 60 (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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58B MET* 3.6 18.2 - - + -
59B GLN* 1.3 79.7 - - - +
61B LYS* 1.3 60.3 + - - +
62B LEU* 4.2 8.8 - - + +
72B THR* 3.8 22.4 - - + -
73B ALA 4.9 0.7 - - - +
74B PHE* 3.9 28.3 - - + -
90B PHE* 3.7 27.8 - - + -
123B PRO 4.5 1.0 - - - +
126B GLU 3.8 1.9 - - - +
127B PHE* 3.5 5.2 - - - -
128B HIS* 2.9 28.2 + - - +
130B TYR* 3.8 25.4 + - + -
198B SER 3.3 6.7 - - - +
199B TYR* 3.7 26.5 - - + +
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Residues in contact with LYS 61 (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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32B GLU* 5.5 0.6 + - - -
60B MET* 1.3 75.2 - - - +
62B LEU* 1.3 67.6 + - - +
64B PRO* 6.0 3.6 - - - +
123B PRO 3.6 3.1 - - - -
124B THR 3.5 27.1 + - - +
125B LYS 3.8 4.5 - - - +
126B GLU* 3.6 31.2 - - - +
127B PHE* 3.6 37.0 - - + +
197B ALA* 3.8 1.9 - - - +
198B SER* 2.9 47.2 + - - +
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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