Contacts of the strand formed by residues 214 - 221 (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 ARG 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.5 14.2 - - - +
53A GLN* 2.7 32.7 + - - +
55A SER* 2.9 26.8 + - - -
56A TYR 4.8 11.4 - - - +
58A GLU 5.2 3.6 - - - +
59A PRO* 5.3 0.9 - - + -
94A PHE* 3.6 22.4 - - + +
95A LEU* 3.4 4.5 - - - -
96A ALA* 2.8 35.8 + - - +
97A PRO 3.2 22.2 - - - +
98A VAL* 3.6 24.3 - - + +
100A SER* 3.0 36.4 + - - -
101A SER 3.8 2.0 + - - +
213A VAL* 1.3 75.1 - - - +
215A ILE* 1.3 60.2 + - - +
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Residues in contact with ILE 215 (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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6A PHE* 4.2 9.9 - - + -
55A SER* 3.0 6.1 - - - -
56A TYR* 2.9 39.5 + - + -
58A GLU 5.6 0.4 + - - -
60A VAL* 3.9 26.4 - - + +
93A PHE* 4.2 10.3 - - + -
94A PHE* 3.4 6.3 - - - +
95A LEU* 3.8 29.4 - - + -
213A VAL* 4.2 8.3 + - + -
214A ARG* 1.3 78.6 - - - +
216A GLY* 1.3 58.2 + - - +
232A TRP* 3.8 14.5 - - + -
234A PHE* 3.5 41.7 - - + -
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Residues in contact with GLY 216 (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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54A ALA 3.2 12.3 - - - -
55A SER* 3.7 1.3 - - - -
93A PHE* 3.5 10.2 - - - -
94A PHE* 2.9 46.8 + - - -
215A ILE* 1.3 76.9 - - - +
217A PHE* 1.3 64.5 + - - -
232A TRP* 4.1 10.1 - - - -
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Residues in contact with PHE 217 (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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35A LEU* 4.5 6.7 - - + -
37A LEU* 3.9 24.0 - - + +
53A GLN* 3.2 6.4 - - - +
54A ALA 2.8 38.2 + - - +
76A PHE* 3.5 46.7 - + + -
91A LEU* 5.0 2.2 - - + -
92A ALA 3.3 9.0 - - - +
93A PHE* 3.8 13.5 - + - -
94A PHE* 3.6 0.8 - - - -
216A GLY* 1.3 77.5 - - - -
218A SER* 1.3 61.1 + - - +
229A ILE* 3.9 29.8 - - + -
232A TRP* 3.4 57.2 - + - -
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Residues in contact with SER 218 (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 1.8 - - - -
52A GLY 3.5 4.2 + - - -
53A GLN* 3.2 27.6 + - - +
91A LEU* 3.3 4.0 - - - +
92A ALA 2.8 33.7 + - - -
94A PHE* 3.8 4.2 - - - -
109A LEU 2.6 24.1 + - - +
110A GLY* 3.5 5.9 - - - -
111A LEU* 3.8 22.7 - - - -
217A PHE* 1.3 74.8 - - - +
219A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 219 (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* 3.6 30.9 - - + +
38A THR* 4.1 13.2 - - + +
51A ALA* 3.3 6.9 - - - +
52A GLY 3.0 29.5 + - - +
90A GLY 3.6 15.0 - - - +
91A LEU* 4.2 3.8 - - + +
109A LEU 3.6 9.7 - - - +
110A GLY* 4.0 0.3 - - - -
218A SER* 1.3 76.1 + - - +
220A GLY* 1.3 59.9 + - - +
221A VAL* 5.9 1.1 - - + -
227A THR* 4.9 5.6 - - - +
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Residues in contact with GLY 220 (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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38A THR* 4.6 0.2 - - - -
50A SER 3.4 7.4 - - - -
51A ALA* 4.4 0.9 - - - -
89A ASP* 3.1 24.9 + - - +
90A GLY 3.6 8.2 + - - +
105A TYR* 4.4 0.2 - - - -
106A GLY 3.8 22.0 - - - -
109A LEU* 3.7 11.1 - - - +
110A GLY 4.3 1.6 - - - -
219A ALA* 1.3 77.6 - - - +
221A VAL* 1.3 65.8 + - - +
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Residues in contact with VAL 221 (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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38A THR* 4.0 17.0 - - + +
47A VAL 3.5 24.5 - - - +
49A SER* 3.3 6.5 - - - +
50A SER* 2.8 47.1 + - - +
88A ALA 3.4 13.7 - - - +
89A ASP 3.8 0.2 - - - +
90A GLY 5.5 0.4 - - - +
105A TYR* 3.6 0.3 - - - -
106A GLY* 2.9 19.1 + - - -
219A ALA* 5.9 0.9 - - + -
220A GLY* 1.3 79.3 - - - +
222A GLY* 1.3 61.6 + - - +
223A TYR* 4.0 0.7 - - - +
225A GLU* 3.5 33.2 - - + +
226A VAL* 5.4 0.2 - - - -
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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