Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 4L1X
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 VAL 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG* 4.2 1.6 - - - +
81A TYR* 3.7 34.3 - - + +
83A SER* 4.2 9.6 - - - -
99A LEU* 4.0 10.5 - - + -
102A SER* 5.8 0.2 - - - -
103A LEU* 3.6 17.7 - - + +
106A LEU* 4.2 4.9 - - + -
110A TYR* 1.3 81.7 - - - +
112A ASP* 1.3 59.7 + - - +
113A LEU 3.5 24.9 - - - +
114A TYR* 4.0 8.1 - - + -
159A LEU 2.9 16.3 + - - +
160A ALA* 3.2 12.0 - - + -
161A LYS 2.9 23.0 + - - -
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Residues in contact with ASP 112 (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 ARG* 2.9 29.5 + - - +
77A GLU* 6.1 0.5 - - - -
79A ILE 3.6 12.0 - - - +
80A PHE* 3.6 27.1 - - + -
81A TYR 2.8 36.6 + - - +
110A TYR* 3.8 13.0 + - - -
111A VAL* 1.3 74.3 - - - +
113A LEU* 1.3 59.6 + - - +
161A LYS* 3.5 14.1 - - + +
162A SER* 2.9 29.2 + - - -
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Residues in contact with LEU 113 (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 MET* 3.7 28.0 - - + -
48A HIS* 5.6 0.9 - - - +
80A PHE* 3.7 8.1 - - + -
81A TYR 3.2 2.8 + - - -
82A THR* 3.3 29.1 - - + +
83A SER 2.9 27.4 + - - +
111A VAL* 3.2 7.0 - - - +
112A ASP* 1.3 80.1 - - - +
114A TYR* 1.3 59.5 + - - +
115A LEU* 3.6 23.8 - - + -
162A SER* 3.3 20.6 - - - +
163A ILE 3.8 2.9 - - - -
187A VAL* 3.5 28.5 - - + -
188A CYS* 3.8 13.2 - - - -
190A GLN* 6.0 1.1 - - - +
214A VAL* 5.9 0.7 - - + -
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Residues in contact with TYR 114 (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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53A HIS* 6.0 0.3 - - - +
83A SER* 3.3 22.7 - - - -
84A LYS 3.6 21.2 + - - -
85A LEU* 3.5 39.0 - - + +
95A VAL* 4.5 5.2 - - + -
98A ALA* 3.6 5.4 + - - +
99A LEU* 3.3 63.7 + - + -
102A SER* 5.0 2.4 + - - -
111A VAL* 4.0 2.5 - - + -
113A LEU* 1.3 73.5 - - - +
115A LEU* 1.3 60.9 - - - +
151A MET* 3.2 33.6 - - + +
154A CYS* 5.3 2.7 - - + -
160A ALA* 3.9 17.9 - - + -
162A SER 3.1 7.4 + - - +
163A ILE* 3.3 4.0 - - + -
164A GLY 2.9 22.0 + - - -
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Residues in contact with LEU 115 (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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82A THR* 4.1 8.7 - - + -
83A SER 3.0 14.0 + - - +
84A LYS* 3.2 21.3 - - + -
85A LEU* 2.8 30.5 + - - +
113A LEU* 3.6 14.8 - - + -
114A TYR* 1.3 75.0 - - - +
116A ILE* 1.3 69.6 + - - +
117A HIS 3.2 0.7 + - - -
151A MET* 3.8 5.4 - - - -
164A GLY* 3.2 27.1 - - - +
165A VAL 3.7 2.5 - - - +
166A SER* 4.2 4.5 - - - -
188A CYS* 3.5 24.5 - - - -
190A GLN* 3.7 39.5 - - + +
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Residues in contact with ILE 116 (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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85A LEU* 4.3 6.1 - - + -
90A HIS* 3.9 26.7 - - + +
115A LEU* 1.3 69.8 - - - +
117A HIS* 1.3 62.8 + - - +
118A PHE 4.1 5.6 - - - +
144A LEU* 4.7 9.4 - - + +
147A THR* 3.8 27.8 - - + -
148A TRP* 3.9 26.0 - - + +
151A MET* 3.8 19.5 - - + +
164A GLY 3.2 10.6 + - - +
165A VAL* 4.5 1.6 - - + -
166A SER* 2.9 30.8 + - - +
168A PHE* 4.0 33.2 - - + -
176A ILE* 5.7 0.9 - - + -
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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