Contacts of the strand formed by residues 71 - 77 (chain A) in PDB entry 1LEI
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 THR 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLY* 1.3 77.3 - - - -
72A VAL* 1.3 63.1 + - - +
101A GLU* 4.0 19.1 + - - +
102A ALA 3.2 13.4 + - - -
103A ASP* 3.6 15.6 + - - +
104A LEU* 3.8 7.1 - - - +
162A GLN 4.9 0.2 - - - -
163A VAL* 3.6 4.5 - - - +
164A THR* 2.7 57.4 + - + +
166A ARG* 4.6 9.2 - - - +
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Residues in contact with VAL 72 (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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61A ILE* 4.4 4.0 - - + -
71A THR* 1.3 81.4 + - - +
73A ARG* 1.3 71.8 + - - +
74A ILE* 4.4 4.5 - - + -
100A TYR* 4.2 5.9 - - + +
101A GLU* 3.5 2.6 - - - +
102A ALA* 3.0 32.6 + - + +
103A ASP 5.1 0.9 - - - -
104A LEU* 3.3 28.0 - - + +
113A PHE* 4.0 35.0 - - + -
161A PHE* 5.0 1.3 - - + -
162A GLN 3.7 3.4 - - - -
163A VAL* 3.7 23.3 - - + +
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Residues in contact with ARG 73 (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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72A VAL* 1.3 75.6 - - - +
74A ILE* 1.3 70.1 + - - +
99A TYR* 3.2 47.2 + - + -
100A TYR 3.4 12.8 - - - +
101A GLU* 3.1 33.3 + - + +
136A THR 5.2 1.6 + - - -
137A ASN 4.2 16.4 + - - -
138A ASN* 4.6 8.9 + - - +
160A CYS 3.4 0.9 - - - +
161A PHE* 3.6 0.7 - - - -
162A GLN* 2.8 73.6 + - + +
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Residues in contact with ILE 74 (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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72A VAL* 4.4 4.9 - - + -
73A ARG* 1.3 78.9 - - - +
75A SER* 1.3 66.0 + - - +
90A LEU* 3.1 22.6 - - + +
99A TYR* 3.3 2.9 - - - +
100A TYR* 2.9 42.1 + - + -
113A PHE* 3.6 35.2 - - + -
116A LEU* 4.1 11.7 - - + -
159A LEU* 4.2 13.9 - - + -
160A CYS 3.1 11.4 - - - +
161A PHE* 3.3 40.2 - - + -
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Residues in contact with SER 75 (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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74A ILE* 1.3 75.7 - - - +
76A LEU* 1.3 70.1 + - - +
90A LEU* 4.2 2.7 - - - -
98A GLY 5.0 0.9 - - - -
99A TYR* 3.9 10.1 - - - +
138A ASN* 3.5 28.9 - - - -
140A PRO* 3.4 16.8 - - - +
159A LEU* 3.7 4.9 - - - -
160A CYS* 2.9 32.1 + - - +
162A GLN* 3.0 20.1 + - - +
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Residues in contact with LEU 76 (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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75A SER* 1.3 85.7 + - - +
77A VAL* 1.3 64.1 + - - +
85A PRO* 3.8 2.3 - - - +
86A HIS* 2.9 33.4 + - + +
88A HIS* 3.8 33.9 - - + +
89A GLU 3.8 22.0 - - - +
90A LEU* 4.0 20.9 - - + +
98A GLY 5.1 1.8 + - - +
118A ILE* 4.3 14.4 - - + -
138A ASN* 5.3 2.5 + - - +
140A PRO* 6.1 0.2 - - - +
157A VAL* 3.9 24.5 - - + -
158A ARG 3.5 3.6 - - - +
159A LEU* 4.0 21.8 - - + -
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Residues in contact with VAL 77 (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 LEU* 1.3 78.1 - - - +
78A THR* 1.3 69.3 + - - +
83A HIS* 3.7 25.1 - - + +
84A ARG 3.3 16.6 - - - +
85A PRO 4.7 0.2 - - - -
86A HIS* 4.0 4.5 - - - -
140A PRO* 4.4 20.4 - - + -
141A PHE* 4.6 3.8 - - + -
157A VAL* 3.7 3.5 - - - +
158A ARG* 2.8 40.3 + - + +
160A CYS* 4.3 13.5 - - + -
179A LEU* 3.6 27.8 - - + -
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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