Contacts of the strand formed by residues 82 - 88 (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 ARG 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLY* 3.1 33.3 + - - +
21A LEU 5.4 0.6 + - - -
22A SER* 3.8 24.2 - - - +
78A LYS* 4.1 2.2 - - - -
79A VAL 2.8 36.4 + - - +
80A ASP 3.3 0.4 - - - +
81A GLY* 1.3 80.1 - - - +
83A VAL* 1.3 88.1 + - - +
84A VAL* 3.2 3.2 + - + +
202B T 3.1 35.0 + - - +
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Residues in contact with VAL 83 (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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76A PRO* 4.5 20.4 - - + -
77A HIS 3.5 12.6 - - - +
78A LYS* 4.1 16.8 - - + +
81A GLY 4.3 0.4 + - - +
82A ARG* 1.3 97.7 + - - +
84A VAL* 1.3 67.9 + - - +
202B T 5.3 0.9 - - - +
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Residues in contact with VAL 84 (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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18A ILE* 3.8 18.2 - - + -
19A GLY 3.4 9.9 - - - +
20A GLY* 3.8 12.6 - - - +
21A LEU* 3.7 25.8 - - + -
34A PHE* 4.5 1.1 - - + -
77A HIS* 2.9 40.2 + - + +
79A VAL* 3.9 23.3 - - + +
82A ARG* 3.7 12.6 - - + +
83A VAL* 1.3 84.3 - - - +
85A GLU* 1.3 61.4 + - - +
86A PRO* 3.5 10.4 - - + +
202B T 5.8 0.4 - - - -
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Residues in contact with GLU 85 (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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18A ILE* 4.5 0.7 - - - -
19A GLY 2.8 30.4 + - - +
84A VAL* 1.3 75.6 - - - +
86A PRO* 1.3 64.0 - - + +
87A LYS* 3.4 31.2 + - + +
103A THR* 3.8 19.7 + - - +
156A HIS* 5.3 7.5 + - - +
202B T 2.8 46.5 + - - +
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Residues in contact with PRO 86 (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* 4.8 3.6 - - + -
17A PHE 3.3 7.9 - - - +
18A ILE* 3.8 21.5 - - + -
34A PHE* 4.6 2.7 - - + -
72A MET* 3.3 33.2 - - - +
75A ARG* 4.6 14.0 - - + -
77A HIS* 3.9 33.9 - - + +
84A VAL* 3.5 13.2 - - + +
85A GLU* 1.3 86.3 - - + +
87A LYS* 1.3 64.2 + - - +
156A HIS* 4.4 7.1 + - - -
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Residues in contact with LYS 87 (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* 3.4 8.3 - - - +
17A PHE* 2.7 54.5 + - + +
72A MET* 4.2 5.3 - - - -
85A GLU* 3.4 39.4 + - + +
86A PRO* 1.3 81.6 - - - +
88A ARG* 1.3 62.7 + - - +
101A HIS* 4.4 16.4 + - - +
103A THR* 4.5 10.0 + - - +
156A HIS* 5.0 8.3 - - + -
160A ASP* 4.8 10.8 - - - +
202B T 3.0 22.8 + - - -
203B A 3.8 22.0 + - - +
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Residues in contact with ARG 88 (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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13A LEU 5.5 3.6 + - - -
15A LYS 4.4 1.3 - - - -
16A LEU* 3.9 11.6 - - - +
65A VAL* 5.0 2.2 + - - +
68A VAL* 3.5 17.5 - - - +
69A ASP* 2.9 31.7 + - - +
72A MET* 3.7 20.7 - - - +
73A ASN* 6.0 0.2 + - - -
87A LYS* 1.3 74.5 - - - +
89A ALA* 1.3 63.2 + - - +
90A VAL* 3.3 6.4 + - - +
157A ASP* 2.8 41.6 + - - +
160A ASP* 3.7 31.7 - - + +
161A LYS* 3.4 23.8 - - - +
164A ILE* 4.1 29.2 - - + +
203B A 3.3 14.4 + - - -
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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