Contacts of the strand formed by residues 104 - 111 (chain A) in PDB entry 1LL8
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 CYS 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A THR* 3.4 30.3 - - + -
14A VAL 3.1 10.1 - - - +
15A ASP* 4.5 0.9 - - - +
22A LEU* 4.7 5.8 - - + -
95A LYS 3.4 0.5 - - - +
96A ARG* 4.0 2.2 - - - -
97A MET* 2.9 25.6 + - - +
98A ARG* 3.1 36.3 - - - +
99A GLN* 4.0 8.7 - - + +
102A ARG* 2.8 10.5 + - - +
103A LEU* 1.3 70.8 - - - +
105A CYS* 1.3 59.2 + - - +
106A VAL* 3.4 15.9 - - - -
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Residues in contact with CYS 105 (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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12A PHE 3.6 1.6 - - - +
14A VAL* 2.6 57.4 + - + +
15A ASP 3.8 9.4 - - - +
16A ALA* 4.1 6.3 - - + +
62A GLU* 5.0 1.8 - - - -
94A MET* 3.3 38.9 - - + +
95A LYS* 3.6 9.4 - - - -
96A ARG* 4.2 31.0 - - - +
103A LEU 3.7 3.4 + - - -
104A CYS* 1.3 71.0 - - - +
106A VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 106 (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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9A LYS* 6.1 0.7 - - - +
11A ILE* 4.5 15.5 - - + -
12A PHE 3.3 7.6 - - - +
13A THR* 4.2 12.1 - - + +
93A TRP 3.0 4.2 - - - +
94A MET* 3.0 22.3 - - - -
95A LYS* 3.0 22.5 + - + +
97A MET* 3.4 41.5 - - + -
99A GLN* 5.1 0.7 - - - +
104A CYS* 3.4 16.6 - - - -
105A CYS* 1.3 75.0 - - - +
107A VAL* 1.3 65.9 + - - +
108A VAL* 4.1 20.2 - - + -
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Residues in contact with VAL 107 (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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10A ALA 2.9 11.3 - - - +
12A PHE* 3.2 23.7 + - + +
44A LEU* 4.0 16.2 - - + -
48A PHE* 4.7 1.8 - - + -
74A PHE* 3.3 34.3 - - + -
92A VAL* 3.8 9.2 - - + -
93A TRP 3.5 1.8 - - - -
94A MET* 3.4 33.7 - - + -
105A CYS 4.3 0.2 + - - -
106A VAL* 1.3 74.4 - - - +
108A VAL* 1.3 63.7 + - - +
109A LEU* 3.5 29.6 - - + -
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Residues in contact with VAL 108 (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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9A LYS* 3.8 31.0 - - + +
10A ALA 2.9 19.1 - - - +
11A ILE* 5.2 1.3 - - - -
91A SER 2.7 21.0 - - - +
92A VAL* 3.8 1.3 - - - -
93A TRP* 3.2 68.8 + - + +
95A LYS* 6.1 0.2 - - + -
106A VAL* 4.1 16.6 - - + -
107A VAL* 1.3 77.5 - - - +
109A LEU* 1.3 57.7 + - - +
110A GLU* 5.3 3.1 - - + +
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Residues in contact with LEU 109 (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 ASN 4.6 2.3 - - - +
10A ALA* 3.1 36.0 + - + +
12A PHE* 3.8 13.0 - - + -
31A LEU* 3.3 32.9 - - + +
48A PHE* 3.3 40.6 - - + -
90A VAL* 4.2 13.0 - - + -
91A SER 3.1 7.0 - - - +
92A VAL* 3.4 27.4 - - + -
107A VAL* 3.5 17.9 - - + -
108A VAL* 1.3 71.9 - - - +
110A GLU* 1.3 62.3 + - - +
111A PRO* 3.8 7.3 - - - +
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Residues in contact with GLU 110 (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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4A ASP* 4.6 20.4 - - + +
90A VAL* 3.8 1.8 - - - -
91A SER* 2.8 50.7 + - - +
93A TRP* 4.6 20.8 + - + +
108A VAL* 4.9 3.1 - - + +
109A LEU* 1.3 74.3 - - - +
111A PRO* 1.3 75.9 - - + +
112A VAL 3.4 0.3 + - - -
114A ARG* 4.5 12.2 - - - +
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Residues in contact with PRO 111 (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 ASN* 5.3 20.0 - - - +
31A LEU* 5.1 12.3 - - + -
88A ILE* 5.4 3.6 - - + -
89A PRO 4.2 0.2 - - - +
90A VAL* 3.6 19.0 - - + -
109A LEU 3.8 7.9 - - - +
110A GLU* 1.3 94.0 - - + +
112A VAL* 1.3 64.4 + - - +
113A GLU 3.5 0.9 + - - -
114A ARG* 3.4 55.6 + - + +
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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