Contacts of the strand formed by residues 15 - 19 (chain A) in PDB entry 1U1L
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 LYS 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.1 37.7 + - - +
12A GLN* 3.7 17.4 + - - +
13A LEU 3.4 2.8 - - - +
14A ARG* 1.3 79.8 - - - +
16A LEU* 1.3 73.6 + - - +
42A ASP* 5.4 0.9 - - - +
59A PHE* 3.8 22.2 - - + -
60A VAL 3.5 5.6 - - - +
61A THR* 3.2 22.2 - - + +
68A VAL* 5.3 1.3 - - - +
88A ARG* 4.4 0.9 - - - -
89A ALA* 3.0 30.6 + - + +
92A ARG* 4.2 5.9 - - - +
204B G 2.7 43.4 + - - +
205B G 3.7 10.5 + - - +
207B T 5.5 0.8 + - - -
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Residues in contact with LEU 16 (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 LYS* 1.3 74.7 - - - +
17A PHE* 1.3 60.6 + - - +
18A ILE* 4.1 12.2 - - + +
34A PHE* 5.5 2.2 - - + -
59A PHE* 3.2 12.1 - - - +
60A VAL* 2.8 48.1 + - + +
62A TYR* 4.3 9.4 - - + -
68A VAL* 3.6 34.3 - - + -
71A ALA* 4.1 20.6 - - + -
72A MET* 3.8 27.8 - - + -
86A PRO* 4.8 2.0 - - + -
87A LYS 3.4 23.3 - - - +
88A ARG* 3.9 9.9 - - - -
89A ALA* 4.3 0.2 - - - -
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Residues in contact with PHE 17 (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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16A LEU* 1.3 73.0 - - - +
18A ILE* 1.3 60.2 + - - +
19A GLY* 3.4 30.1 - - - -
57A PHE* 3.6 24.2 - + + -
58A GLY 3.7 5.2 - - - -
59A PHE* 3.8 19.7 - + + -
86A PRO* 3.3 3.1 - - - +
87A LYS* 2.7 56.2 + - + +
89A ALA* 4.1 2.0 - - - +
202B T 4.0 22.0 - - - -
203B A 3.5 75.2 - + + +
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Residues in contact with ILE 18 (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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16A LEU* 4.1 7.2 - - + +
17A PHE* 1.3 86.9 - - - +
19A GLY* 1.3 59.3 + - - +
21A LEU* 3.4 28.0 - - + +
30A LEU* 4.4 2.7 - - + -
34A PHE* 3.7 30.5 - - + -
57A PHE* 3.3 5.2 - - - -
58A GLY 2.8 40.3 + - - +
60A VAL* 3.9 31.9 - - + +
84A VAL* 3.8 24.0 - - + -
85A GLU 3.9 2.5 - - - +
86A PRO* 3.8 16.4 - - + -
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Residues in contact with GLY 19 (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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17A PHE* 3.4 21.4 - - - -
18A ILE* 1.3 71.4 - - - +
20A GLY* 1.3 64.7 + - - -
21A LEU 3.3 3.7 + - - -
57A PHE* 4.2 1.6 - - - -
84A VAL* 3.4 5.2 - - - +
85A GLU 2.8 34.9 + - - -
202B T 3.7 19.1 - - - -
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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