Contacts of the strand formed by residues 90 - 96 (chain A) in PDB entry 1LEC
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 GLY 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU* 4.8 0.7 - - - -
89A ASP* 1.3 80.2 - - - +
91A LEU* 1.3 67.4 + - - +
109A LEU* 3.7 5.6 - - - -
130A PHE 3.0 12.6 - - - -
132A THR* 3.4 9.6 + - - -
219A ALA* 3.6 16.3 - - - +
220A GLY 3.6 9.7 + - - +
221A VAL* 5.5 0.2 - - - +
225A GLU* 3.0 16.5 + - - +
227A THR* 4.6 1.7 + - - -
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Residues in contact with LEU 91 (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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37A LEU* 4.5 4.3 - - + -
76A PHE* 4.6 6.5 - - + -
78A PHE* 4.1 20.0 - - + -
80A LEU* 4.1 18.6 - - + -
90A GLY* 1.3 76.2 - - - +
92A ALA* 1.3 72.1 + - - +
109A LEU* 4.1 5.8 - - - +
129A GLU* 3.5 3.3 - - - +
130A PHE* 3.0 61.4 + - + +
217A PHE* 5.0 1.3 - - + -
218A SER 3.3 12.6 - - - +
219A ALA* 4.2 4.7 - - + +
227A THR* 3.7 39.7 - - + +
229A ILE* 4.4 14.4 - - + -
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Residues in contact with ALA 92 (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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91A LEU* 1.3 82.9 - - - +
93A PHE* 1.3 65.2 + - - +
94A PHE* 5.2 0.2 - - + -
109A LEU* 4.5 4.9 - - + -
111A LEU* 3.9 28.0 - - + -
127A ALA* 4.3 1.8 - - + -
128A VAL 3.1 13.7 - - - +
129A GLU* 4.1 8.5 - - + -
130A PHE* 4.6 1.1 - - - -
217A PHE* 3.3 10.6 - - - +
218A SER* 2.8 40.5 + - - +
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Residues in contact with PHE 93 (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 PHE* 4.7 9.0 - + - -
74A THR* 3.9 24.0 - - + -
76A PHE* 4.2 14.4 - + + -
92A ALA* 1.3 74.3 - - - +
94A PHE* 1.3 71.7 + - - +
95A LEU* 4.1 18.8 - - + -
127A ALA* 3.2 3.8 - - - +
128A VAL* 2.8 38.1 + - + +
130A PHE* 4.6 2.0 - - + -
176A ILE* 3.7 34.1 - - + -
215A ILE* 4.2 14.6 - - + -
216A GLY 3.5 17.3 - - - -
217A PHE* 3.8 17.9 - + - -
232A TRP* 4.0 24.0 - + - -
234A PHE* 4.8 6.5 - + - -
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Residues in contact with PHE 94 (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 GLN* 3.7 9.0 - - + -
55A SER* 4.2 2.2 - - - -
92A ALA 4.4 0.2 - - - -
93A PHE* 1.3 80.6 - - - +
95A LEU* 1.3 70.6 + - - +
96A ALA* 3.6 21.5 - - + -
111A LEU* 3.7 20.0 - - + -
125A VAL* 4.2 2.9 - - + -
126A VAL 3.3 10.3 - - - +
127A ALA* 4.0 6.5 - - + -
214A ARG* 3.6 51.1 - - + -
215A ILE* 3.4 6.1 - - - +
216A GLY* 2.9 70.2 + - - -
217A PHE 3.5 13.5 - - - -
218A SER* 3.8 23.3 - - - -
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Residues in contact with LEU 95 (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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60A VAL* 5.8 1.1 - - + -
62A LEU* 4.5 9.2 - - + -
72A PHE* 4.0 37.9 - - + -
93A PHE* 4.1 13.2 - - + -
94A PHE* 1.3 79.6 - - - +
96A ALA* 1.3 62.5 + - - +
125A VAL* 3.4 4.0 - - - +
126A VAL* 2.9 52.1 + - + +
127A ALA* 5.7 0.4 - - - -
185A LEU* 5.7 2.5 - - + -
205A LEU* 4.9 3.8 - - + -
209A LEU* 3.7 21.8 - - + +
213A VAL* 4.0 15.3 - - + -
214A ARG 3.4 6.5 - - - +
215A ILE* 3.8 20.2 - - + -
234A PHE* 5.8 0.7 - - + -
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Residues in contact with ALA 96 (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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94A PHE* 3.6 22.0 - - + -
95A LEU* 1.3 77.6 - - - +
97A PRO* 1.3 69.8 - - + +
100A SER* 3.6 15.3 - - - +
111A LEU* 5.9 0.9 - - + -
124A GLN 4.0 5.6 - - - +
125A VAL* 4.3 8.1 - - + -
209A LEU* 4.5 2.0 - - - -
213A VAL* 3.2 10.7 - - - +
214A ARG* 2.8 33.9 + - + +
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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