Contacts of the strand formed by residues 12 - 19 (chain B) in PDB entry 3UMO
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 SER 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ALA 5.2 0.4 - - - -
11B PRO* 1.3 77.7 - - - +
13B LEU* 1.3 59.3 + - - +
14B ASP* 2.5 30.2 + - - -
38B GLY* 2.9 37.4 + - - +
39B GLY 4.1 1.0 + - - -
69B LEU* 3.6 9.9 - - - +
89B THR* 3.9 7.0 - - - -
90B ARG* 3.2 18.4 - - - -
92B ASN* 3.7 17.4 + - - -
110B GLY* 6.1 0.9 - - - -
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Residues in contact with LEU 13 (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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88A TRP* 3.9 32.3 - - + -
12B SER* 1.3 70.7 - - - +
14B ASP* 1.3 61.8 + - - +
35B PHE* 3.9 21.3 - - + -
36B GLU 3.9 4.9 - - - +
65B THR* 3.7 36.1 - - + +
68B HIS* 4.0 5.2 - - + -
69B LEU* 4.0 19.1 - - + +
72B LEU* 3.7 30.3 - - + -
89B THR* 3.8 3.9 - - + +
90B ARG 2.9 10.6 + - - +
91B GLN* 3.2 29.1 + - + +
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Residues in contact with ASP 14 (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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12B SER* 2.5 28.8 + - - -
13B LEU* 1.3 74.1 - - - +
15B SER* 1.3 62.7 + - - +
16B ALA 4.1 0.2 - - - -
34B VAL 3.7 0.3 - - - +
35B PHE* 3.2 8.8 - - - -
36B GLU* 2.9 52.5 + - + +
37B PRO 4.5 0.9 - - - +
38B GLY* 3.6 15.1 - - - -
92B ASN* 3.3 34.3 + - - +
94B HIS* 6.0 3.4 - - + +
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Residues in contact with SER 15 (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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108A MET* 4.7 3.7 - - - +
13B LEU 3.9 0.2 + - - -
14B ASP* 1.3 73.1 - - - +
16B ALA* 1.3 60.7 + - - +
17B THR 4.0 0.2 - - - -
33B PRO* 3.7 18.1 - - - +
34B VAL 3.8 3.1 - - - -
35B PHE* 3.1 26.1 - - - -
36B GLU* 5.8 0.2 - - - -
91B GLN* 3.8 12.6 + - - +
92B ASN 2.9 9.8 + - - -
93B LEU* 3.5 19.1 - - - +
94B HIS* 2.8 30.2 + - - +
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Residues in contact with ALA 16 (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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14B ASP 4.1 0.2 - - - -
15B SER* 1.3 71.0 - - - +
17B THR* 1.3 61.2 + - - +
18B ILE* 5.8 0.2 - - - -
32B ALA 4.5 0.7 - - - +
33B PRO* 3.3 2.5 - - - +
34B VAL* 2.9 51.6 + - + +
36B GLU* 3.9 19.5 - - - +
94B HIS* 3.4 22.2 - - + +
292B THR* 5.8 0.2 - - + -
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Residues in contact with THR 17 (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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108A MET* 4.1 10.8 - - - -
16B ALA* 1.3 74.5 - - - +
18B ILE* 1.3 74.0 + - - +
30B CYS* 3.1 19.7 - - + +
31B THR* 2.7 39.0 + - - -
33B PRO* 4.5 1.3 - - - -
93B LEU* 3.9 20.2 - - + -
94B HIS* 2.9 17.4 + - - +
95B VAL* 3.5 13.6 - - + -
96B HIS* 2.8 26.2 + - - +
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Residues in contact with ILE 18 (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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16B ALA 5.7 0.4 - - - +
17B THR* 1.3 85.8 + - - +
19B THR* 1.3 70.3 + - - +
29B ARG 4.0 0.5 - - - +
30B CYS* 3.3 4.9 - - - -
31B THR* 2.9 48.8 + - + +
96B HIS* 3.4 22.2 - - + +
98B GLU* 3.7 28.3 - - + +
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Residues in contact with THR 19 (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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106A PHE* 5.3 0.4 - - + -
18B ILE* 1.3 78.8 - - - +
20B PRO* 1.3 70.0 - - - +
21B GLN 3.4 20.0 + - - +
22B ILE* 5.4 0.4 - - + -
28B LEU* 4.0 14.6 - - + +
29B ARG 2.8 27.6 + - - -
30B CYS* 3.9 11.7 - - - -
95B VAL* 3.8 23.1 - - + -
96B HIS 3.0 7.7 + - - +
97B VAL* 3.3 7.6 - - + -
98B GLU 2.9 22.1 + - - -
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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