Contacts of the strand formed by residues 104 - 111 (chain M) in PDB entry 1UW9
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 104 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M PHE* 3.4 33.2 - + - -
44M PHE* 3.1 8.5 - - - +
45M ALA 2.8 34.7 + - - +
47M ALA* 3.8 22.1 - - + +
50M ALA* 3.6 24.7 - - + -
51M TYR* 4.1 5.8 + + - -
73M TRP* 3.5 20.6 - - + -
103M ALA* 1.3 72.9 - - - +
105M VAL* 1.3 58.4 + - - +
122M LEU* 4.0 6.1 - - + -
124M GLN 3.3 3.8 - - - -
125M ARG* 3.6 28.3 + - + -
126M PRO* 3.5 22.9 - - + -
129M ALA* 3.6 19.4 - - - +
131M ASP* 3.8 17.5 + - - -
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Residues in contact with VAL 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M LEU* 4.0 13.2 - - + -
43M GLU 3.4 10.8 - - - +
44M PHE* 4.0 10.8 - - + -
73M TRP* 4.1 0.4 - - - -
93M ILE* 5.7 0.4 - - + +
96M CYS* 3.8 26.9 - - + +
97M THR* 4.1 10.5 - - + -
100M PHE* 4.6 2.7 - - + +
103M ALA* 4.1 4.5 - - + +
104M TYR* 1.3 79.7 - - - +
106M ARG* 1.3 62.8 + - - +
122M LEU* 3.3 7.2 - - - +
123M VAL* 2.8 38.2 + - + -
124M GLN* 2.9 43.6 + - + +
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Residues in contact with ARG 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M PHE* 5.3 5.2 - - + -
42M LEU* 3.5 8.5 - - - +
43M GLU* 2.8 61.6 + - - +
70M ASN 5.3 0.4 + - - -
71M ARG 3.0 23.0 + - - -
72M TYR* 4.7 0.2 - - - +
73M TRP* 3.3 61.5 - - + +
105M VAL* 1.3 74.8 - - - +
107M LEU* 1.3 59.4 + - - +
108M VAL* 4.0 16.1 + - + +
117M GLN* 5.8 1.5 - - - +
120M GLY* 6.4 0.2 - - - -
121M PHE 3.4 20.6 - - - +
122M LEU* 4.1 4.5 - - + -
123M VAL* 4.1 1.1 - - - +
183O LYS* 5.9 0.4 - - - +
187O ARG* 5.9 0.2 - - - +
163R ASN* 4.0 20.6 + - - +
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Residues in contact with LEU 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M ILE* 5.4 0.2 - - + -
30M VAL* 3.8 28.5 - - + -
33M ILE* 3.9 17.7 - - + -
40M PRO* 4.6 1.3 - - + -
41M CYS 3.6 20.4 - - - +
42M LEU* 3.9 16.6 - - + +
80M MET* 6.4 0.2 - - - -
89M VAL* 3.8 20.9 - - + -
93M ILE* 4.4 9.4 - - + -
106M ARG* 1.3 73.1 - - - +
108M VAL* 1.3 69.7 + - - +
119M MET* 4.4 1.5 - - - +
120M GLY* 3.1 3.8 - - - -
121M PHE* 3.0 53.1 + - + +
123M VAL* 4.0 16.4 - - + +
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Residues in contact with VAL 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ILE* 4.6 0.2 - - - +
40M PRO* 3.5 2.4 - - - +
41M CYS* 2.9 52.3 + - + +
43M GLU* 3.8 24.5 - - + +
106M ARG* 4.0 18.2 - - + +
107M LEU* 1.3 85.0 - - - +
109M ALA* 1.3 63.1 + - - +
110M PHE* 3.9 21.3 - - + -
117M GLN* 3.3 31.9 - - - +
119M MET* 3.4 9.4 - - - -
120M GLY* 4.1 2.0 - - - -
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Residues in contact with ALA 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ILE* 3.8 25.8 - - + -
38M TRP* 4.0 9.6 - - + -
39M ILE 3.0 12.1 - - - +
108M VAL* 1.3 78.7 - - - +
110M PHE* 1.3 64.9 + - - +
117M GLN* 3.4 5.4 - - - +
118M ILE* 2.8 26.8 + - + +
119M MET* 3.2 27.5 + - + -
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Residues in contact with PHE 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M TRP* 3.4 6.8 - - - +
39M ILE* 2.8 57.5 + - + +
41M CYS* 3.6 30.7 - - + -
43M GLU* 4.8 1.6 - - - -
75M MET* 5.7 0.4 - - + -
79M PRO* 4.4 12.6 - - + -
108M VAL* 3.9 12.3 - - + -
109M ALA* 1.3 73.9 - - - +
111M ASP* 1.3 62.8 + - - +
112M ASN* 4.0 0.4 - - - -
116M VAL 3.7 3.8 - - - +
117M GLN* 3.7 34.8 - - + -
118M ILE* 4.2 3.4 - - - -
184O ASN* 4.9 4.9 - - - -
187O ARG* 3.7 44.2 - - - -
74V LEU* 4.0 24.2 - - + +
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Residues in contact with ASP 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M TRP* 3.3 28.9 + - + -
110M PHE* 1.3 75.3 - - - +
112M ASN* 1.3 58.8 + - - +
113M GLN* 2.7 39.0 + - - +
114M LYS* 2.9 29.3 + - + +
115M GLN* 2.9 26.7 + - - -
116M VAL 2.9 15.4 + - - +
118M ILE* 4.0 17.5 - - + +
74V LEU 4.4 0.3 - - - +
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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