Contacts of the strand formed by residues 195 - 208 (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 PHE 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A HIS* 3.4 3.5 - - - -
37A LEU* 2.9 61.7 + - + +
63A VAL* 3.9 22.9 - - + -
66A ASP* 3.1 31.0 - - - -
67A SER* 4.3 4.0 - - - -
68A ALA 5.1 0.4 - - - -
70A THR* 4.0 11.0 - - + -
173A LEU* 3.3 8.8 - - + +
188A THR* 3.5 33.9 - - + -
189A ASP 3.5 17.5 - - - -
190A TRP* 3.8 16.2 - + - -
192A LYS* 3.8 20.4 - - + -
193A ALA* 4.1 7.2 - - + -
194A PRO* 1.3 71.6 - - - +
196A ILE* 1.3 58.8 + - - +
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Residues in contact with ILE 196 (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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34A GLN* 3.7 42.2 - - + +
35A LEU 3.3 2.5 - - - +
36A HIS* 3.5 33.4 - - + +
61A LYS 4.7 0.2 - - - +
62A LEU 4.0 1.4 - - - +
63A VAL* 3.4 27.0 + - - +
64A PRO* 3.7 11.5 - - + +
194A PRO* 3.8 19.2 + - + +
195A PHE* 1.3 78.2 - - - +
197A ALA* 1.3 62.7 + - - +
198A SER* 4.3 4.4 + - - +
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Residues in contact with ALA 197 (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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34A GLN* 3.3 2.3 - - - -
35A LEU* 2.7 38.6 + - + +
60A MET* 5.9 0.2 - - + -
61A LYS 3.8 7.9 - - - +
62A LEU* 5.0 0.9 - - + -
63A VAL* 4.0 8.7 - - + +
72A THR* 3.8 35.4 - - + +
173A LEU* 4.1 10.5 - - + +
196A ILE* 1.3 74.8 - - - +
198A SER* 1.3 60.9 + - - +
199A TYR* 3.8 12.3 - - + +
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Residues in contact with SER 198 (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* 4.2 6.4 + - - -
33A ILE 3.3 8.5 - - - -
34A GLN* 3.7 18.2 + - - +
60A MET* 3.2 5.7 - - - +
61A LYS* 2.9 47.5 + - - +
127A PHE* 3.6 24.9 - - - -
196A ILE* 4.3 5.5 + - - +
197A ALA* 1.3 74.7 - - - +
199A TYR* 1.3 66.2 + - - +
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Residues in contact with TYR 199 (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* 3.3 6.2 - - - +
33A ILE* 2.9 49.6 + - + -
35A LEU* 3.6 35.9 - - + +
45A PHE* 3.9 6.7 - + - -
58A MET* 3.5 25.8 - - + -
59A GLN 3.2 5.4 - - - +
60A MET* 3.7 21.8 - - + -
72A THR* 3.3 20.3 - - + +
73A ALA 3.8 0.9 + - - -
74A PHE* 5.3 0.2 - - + -
127A PHE* 4.0 0.9 - - - -
171A SER* 2.5 35.1 + - - -
172A SER 3.9 1.4 + - - -
197A ALA* 3.8 21.8 - - + -
198A SER* 1.3 80.0 - - - +
200A ARG* 1.3 63.1 + - - +
202A PHE* 3.6 11.3 - - + -
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Residues in contact with ARG 200 (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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8A ASP* 5.9 0.4 - - - -
31A ASN 3.6 18.6 - - - +
32A GLU* 2.8 29.6 + - + +
58A MET* 3.7 4.9 - - - +
59A GLN* 2.8 52.2 + - + +
61A LYS* 5.6 0.4 - - - +
127A PHE* 3.5 39.7 - - + +
199A TYR* 1.3 79.0 - - - +
201A SER* 1.3 64.0 + - - +
202A PHE* 3.1 12.5 + - - -
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Residues in contact with SER 201 (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* 4.6 1.0 - - - +
7A VAL 3.9 1.4 + - - +
8A ASP* 2.7 39.0 + - - +
9A VAL* 3.0 24.5 + - - +
31A ASN 4.1 2.8 + - - -
57A SER 4.3 2.0 + - - -
59A GLN* 3.9 18.2 - - - -
129A TYR* 3.8 11.7 - - - -
200A ARG* 1.3 77.1 - - - +
202A PHE* 1.3 75.1 + - - +
203A HIS* 3.1 17.1 + - - +
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Residues in contact with PHE 202 (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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9A VAL* 3.4 27.5 - - + +
10A ALA 4.5 0.4 - - - +
11A PHE* 3.5 31.6 - + + -
14A ASN* 2.9 22.7 - - - +
15A TYR* 3.8 35.6 - + + -
30A GLY 3.4 20.6 - - - -
31A ASN 3.7 14.8 - - - -
33A ILE* 3.8 15.9 - - + -
45A PHE* 4.4 3.6 - + - -
57A SER 3.9 1.0 + - - -
58A MET* 3.5 30.4 - - + -
199A TYR* 3.6 28.5 - - + -
200A ARG* 3.1 9.0 + - - -
201A SER* 1.3 74.5 - - - +
203A HIS* 1.3 60.4 + - - +
204A ILE 3.5 0.2 + - - -
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Residues in contact with HIS 203 (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 17.4 - - + +
7A VAL* 3.4 37.2 + - + +
9A VAL* 5.0 1.8 - - + -
14A ASN* 4.6 0.4 - - - -
15A TYR* 4.8 1.9 + - - -
55A HIS* 3.6 31.0 + - - -
56A PHE* 3.6 2.1 - - - -
57A SER* 3.0 48.7 + - - +
201A SER* 3.1 16.3 + - - +
202A PHE* 1.3 75.4 - - - +
204A ILE* 1.3 68.3 + - - +
205A ASP* 3.8 26.5 + - + +
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Residues in contact with ILE 204 (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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14A ASN* 3.8 33.1 + - + +
15A TYR* 3.6 30.3 - - + +
47A SER* 4.0 10.3 - - - -
51A TYR* 3.5 39.9 - - + +
55A HIS 4.0 2.5 - - - -
56A PHE* 3.8 16.4 - - + -
169A ILE* 3.6 19.3 - - + -
202A PHE 3.5 3.5 + - - +
203A HIS* 1.3 84.6 + - - +
205A ASP* 1.3 63.8 + - - +
206A GLY 4.2 1.3 + - - +
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Residues in contact with ASP 205 (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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55A HIS* 2.8 42.0 + - + +
56A PHE* 5.0 0.2 - - - -
203A HIS* 3.8 20.1 + - + +
204A ILE* 1.3 74.3 - - - +
206A GLY* 1.3 57.8 + - - +
222A ARG* 4.2 9.2 + - - -
223A TRP* 2.8 35.2 + - - -
224A TRP* 3.2 16.4 - - - -
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Residues in contact with GLY 206 (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* 3.7 17.5 - - - -
53A PHE 3.5 9.4 - - - -
54A GLY* 3.8 1.8 - - - -
56A PHE* 4.5 3.4 - - - -
204A ILE* 4.0 5.7 - - - +
205A ASP* 1.3 78.1 + - - +
207A CYS* 1.3 60.6 + - - -
208A GLU* 3.2 8.5 + - - +
222A ARG* 3.7 12.0 + - - -
224A TRP* 3.5 11.7 - - - -
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Residues in contact with CYS 207 (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 2.5 - - - -
52A LEU 2.9 42.9 + - - +
53A PHE* 3.0 9.5 + - + +
206A GLY* 1.3 69.1 - - - -
208A GLU* 1.3 67.6 + - - +
209A ALA* 3.3 2.3 + - - +
216A CYS* 2.2 43.1 - - + -
218A THR* 3.7 3.6 - - - -
219A GLN* 4.2 16.2 - - - +
222A ARG* 3.4 29.2 - - - +
224A TRP* 3.7 5.6 - - + -
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Residues in contact with GLU 208 (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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49A GLY* 3.9 19.7 - - - -
50A SER 3.4 8.8 + - - +
51A TYR* 3.5 25.1 - - + +
206A GLY 3.2 8.1 + - - +
207A CYS* 1.3 71.9 - - - +
209A ALA* 1.4 59.6 + - - +
215A PHE 4.1 0.5 - - - +
216A CYS* 3.6 18.5 - - - +
222A ARG* 4.8 1.0 - - - +
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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